Package org.sbml.jsbml.ext.comp

Class ReplacedElement

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.comp.SBaseRef

org.sbml.jsbml.ext.comp.ReplacedElement

All Implemented Interfaces:

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

public class ReplacedElement
extends SBaseRef

Points to a submodel object that should be considered "replaced".

The object holding the ReplacedElement instance is the one doing the replacing; the object pointed to by the ReplacedElement object is the object being replaced.

Since:

1.0

Author:

Nicolas Rodriguez

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
ReplacedElement()	Creates an ReplacedElement instance
ReplacedElement(int level, int version)	Creates a ReplacedElement instance with a level and version
ReplacedElement(ReplacedElement obj)	Clone constructor

Method Summary

Modifier and Type	Method	Description
ReplacedElement	clone()	clones this class
boolean	equals(java.lang.Object obj)
java.lang.String	getConversionFactor()	Returns the value of conversionFactor
java.lang.String	getDeletion()	Returns the value of deletion
java.lang.String	getSubmodelRef()	Returns the value of submodelRef
int	hashCode()
void	initDefaults()	Initializes the default values using the namespace.
boolean	isSetConversionFactor()	Returns whether conversionFactor is set
boolean	isSetDeletion()	Returns whether deletion is set
boolean	isSetSubmodelRef()	Returns whether submodelRef is set
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
void	setConversionFactor(java.lang.String conversionFactor)	Sets the value of the optional conversionFactor attribute.
void	setDeletion(java.lang.String deletion)	Sets the value of the optional deletion attribute.
void	setSubmodelRef(java.lang.String submodelRef)	Sets the value of the required submodelRef attribute.
boolean	unsetConversionFactor()	Unsets the variable conversionFactor
boolean	unsetDeletion()	Unsets the variable deletion
boolean	unsetSubmodelRef()	Unsets the variable submodelRef
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes()

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, 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, 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.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

removeTreeNodeChangeListener

Methods inherited from class org.sbml.jsbml.ext.comp.SBaseRef

createSBaseRef, getAllowsChildren, getChildAt, getChildCount, getIdRef, getMetaIdRef, getPortRef, getSBaseRef, getUnitRef, isSetIdRef, isSetMetaIdRef, isSetPortRef, isSetSBaseRef, isSetUnitRef, setIdRef, setMetaIdRef, setPortRef, setSBaseRef, setUnitRef, unsetIdRef, unsetMetaIdRef, unsetPortRef, unsetSBaseRef, unsetUnitRef

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, isLeaf

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

Constructor Detail

ReplacedElement

public ReplacedElement()

Creates an ReplacedElement instance

ReplacedElement

public ReplacedElement(int level,
                       int version)

Creates a ReplacedElement instance with a level and version. -

Parameters:

level - the SBML level

version - the SBML version

ReplacedElement

public ReplacedElement(ReplacedElement obj)

Clone constructor

Parameters:

obj - the instance to clone

Method Detail

clone

public ReplacedElement clone()

clones this class

Specified by:

clone in interface SBase

Overrides:

clone in class SBaseRef

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

Overrides:

initDefaults in class SBaseRef

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class SBaseRef

equals

public boolean equals(java.lang.Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class SBaseRef

getSubmodelRef

public java.lang.String getSubmodelRef()

Returns the value of submodelRef

Returns:

the value of submodelRef

isSetSubmodelRef

public boolean isSetSubmodelRef()

Returns whether submodelRef is set

Returns:

whether submodelRef is set

setSubmodelRef

public void setSubmodelRef(java.lang.String submodelRef)

Sets the value of the required submodelRef attribute.

The required attribute submodelRef takes a value which must be the identifier of a Submodel object in the containing model. This attribute is analogous to the corresponding attribute on ReplacedElement; that is, the model referenced by the Submodel object establishes the object namespaces for the portRef, idRef, unitRef and metaIdRef attributes: only objects within the Model object may be referenced by those attributes.

Parameters:

submodelRef - the value of submodelRef

unsetSubmodelRef

public boolean unsetSubmodelRef()

Unsets the variable submodelRef

Returns:

true, if submodelRef was set before, otherwise false

getDeletion

public java.lang.String getDeletion()

Returns the value of deletion

Returns:

the value of deletion

isSetDeletion

public boolean isSetDeletion()

Returns whether deletion is set

Returns:

whether deletion is set

setDeletion

public void setDeletion(java.lang.String deletion)

Sets the value of the optional deletion attribute.

The optional attribute deletion takes a value that must be the identifier of a Deletion object in the parentModel of the ReplacedElement (i.e., the value of some Deletion object's id attribute). When deletion is set, it means the ReplacedElement object is actually an annotation to indicate that the replacement object replaces something deleted from a submodel. The use of the deletion attribute overrides the use of the attributes inherited from SBaseRef: instead of using portRef or idRef, the ReplacedElement instance sets deletion to the identifier of the Deletion object. In addition, the referenced Deletion must be a child of the Submodel referenced by the submodelRef attribute.

Parameters:

deletion - the value of deletion

unsetDeletion

public boolean unsetDeletion()

Unsets the variable deletion

Returns:

true, if deletion was set before, otherwise false

getConversionFactor

public java.lang.String getConversionFactor()

Returns the value of conversionFactor

Returns:

the value of conversionFactor

isSetConversionFactor

public boolean isSetConversionFactor()

Returns whether conversionFactor is set

Returns:

whether conversionFactor is set

setConversionFactor

public void setConversionFactor(java.lang.String conversionFactor)

Sets the value of the optional conversionFactor attribute.

The ReplacedElement class's conversionFactor attribute, if present, defines how to transform or rescale the replaced object's value so that it is appropriate for the new contexts in which the object appears. This attribute takes a value that must refer to a Parameter object instance defined in the model. This parameter then acts as a conversion factor.

Parameters:

conversionFactor - the value of conversionFactor

unsetConversionFactor

public boolean unsetConversionFactor()

Unsets the variable conversionFactor

Returns:

true, if conversionFactor was set before, otherwise false

writeXMLAttributes

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

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class SBaseRef

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class SBaseRef