org.sbml.jsbml.ext.multi

Class Bond

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.multi.Bond

All Implemented Interfaces:

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

public class Bond
extends AbstractSBase

Since:

1.0

Version:

$Rev: 1639 $

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Bond.BOND_OCCURRENCE_TYPE

Field Summary

Fields

Modifier and Type	Field and Description
private BindingSiteReference	bindingSiteReference1
private BindingSiteReference	bindingSiteReference2
private Bond.BOND_OCCURRENCE_TYPE	occurence
private static long	serialVersionUID Generated serial version identifier.

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
Bond()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	addBindingSiteReference(BindingSiteReference bindingSiteReference) Adds a BindingSiteReference to this Bond.
AbstractSBase	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
BindingSiteReference	getBindingSiteReference1() Returns the first BindingSiteReference
BindingSiteReference	getBindingSiteReference2() Returns the second BindingSiteReference.
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
Bond.BOND_OCCURRENCE_TYPE	getOccurence() Returns the occurrence.
void	initDefaults()
boolean	isSetBindingSiteReference1() Returns true if the first BindingSiteReference is set.
boolean	isSetBindingSiteReference2() Returns true if the second BindingSiteReference is set.
boolean	isSetOccurence() Returns true if the occurrence is set.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setBindingSiteReference1(BindingSiteReference bindingSite1) Sets the first BindingSiteReference.
void	setBindingSiteReference2(BindingSiteReference bindingSiteReference2) Sets the second BindingSiteReference.
void	setOccurence(Bond.BOND_OCCURRENCE_TYPE occurence) Sets the occurrence.
java.lang.String	toString()
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes() Returns a map with all the attributes of this SBase that need to be written out in XML.

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, equals, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, 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

removeTreeNodeChangeListener

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

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

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

occurence

private Bond.BOND_OCCURRENCE_TYPE occurence

bindingSiteReference1

private BindingSiteReference bindingSiteReference1

bindingSiteReference2

private BindingSiteReference bindingSiteReference2

Constructor Detail

Bond

public Bond()

Method Detail

clone

public AbstractSBase 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 AbstractSBase

Returns:

a copy of this object

getOccurence

public Bond.BOND_OCCURRENCE_TYPE getOccurence()

Returns the occurrence.

Returns:

the occurrence

setOccurence

public void setOccurence(Bond.BOND_OCCURRENCE_TYPE occurence)

Sets the occurrence.

Parameters:

occurrence - the occurrence to set

isSetOccurence

public boolean isSetOccurence()

Returns true if the occurrence is set.

Returns:

true if the occurrence is set.

getBindingSiteReference1

public BindingSiteReference getBindingSiteReference1()

Returns the first BindingSiteReference

Returns:

the first BindingSiteReference

setBindingSiteReference1

public void setBindingSiteReference1(BindingSiteReference bindingSite1)

Sets the first BindingSiteReference.

Parameters:

bindingSiteReference1 - the BindingSiteReference to set

isSetBindingSiteReference1

public boolean isSetBindingSiteReference1()

Returns true if the first BindingSiteReference is set.

Returns:

true if the first BindingSiteReference is set.

getBindingSiteReference2

public BindingSiteReference getBindingSiteReference2()

Returns the second BindingSiteReference.

Returns:

the second BindingSiteReference.

setBindingSiteReference2

public void setBindingSiteReference2(BindingSiteReference bindingSiteReference2)

Sets the second BindingSiteReference.

Parameters:

bindingSiteReference2 - the BindingSiteReference to set

isSetBindingSiteReference2

public boolean isSetBindingSiteReference2()

Returns true if the second BindingSiteReference is set.

Returns:

true if the second BindingSiteReference is set.

addBindingSiteReference

public boolean addBindingSiteReference(BindingSiteReference bindingSiteReference)

Adds a BindingSiteReference to this Bond. If there are already two BindingSiteReferences, the new BindingSiteReference is not added and false is returned.

Parameters:

bindingSiteReference -

Returns:

true is the BindingSiteReference was added successfully to the Bond.

toString

public java.lang.String toString()

Specified by:

toString in class AbstractSBase

initDefaults

public void initDefaults()

getChildAt

public javax.swing.tree.TreeNode getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class AbstractSBase

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBase

Returns a map with all the attributes of this SBase that need to be written out in XML.

The attribute name is used as a key and the attribute value as value. If a prefix is needed for the attribute name, it need to be set directly in this map.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

Returns:

a Map containing the XML attributes of this object.