org.sbml.jsbml

Class AbstractNamedSBaseWithUnit

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.AbstractNamedSBaseWithUnit

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, NamedSBaseWithDerivedUnit, SBase, SBaseWithDerivedUnit, SBaseWithUnit, TreeNodeWithChangeSupport

Direct Known Subclasses:

Event, QuantityWithUnit

public abstract class AbstractNamedSBaseWithUnit
extends AbstractNamedSBase
implements NamedSBaseWithDerivedUnit, SBaseWithUnit

This simple implementation of the interfaces NamedSBaseWithDerivedUnit and SBaseWithUnit defines elements that can be addressed by their identifier and are or can be associated with a defined Unit or UnitDefinition. Derived elements from this class might be directly or indirectly associated with some value, i.e., the value might be derived by evaluating some expression in form of an ASTNode, or it might be directly defined as an attribute.

Since:

0.8

Version:

$Rev$

Author:

Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private static org.apache.log4j.Logger	logger Log4j logger
private static long	serialVersionUID
protected java.lang.String	unitsID The unit attribute of this variable.

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, lv, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
AbstractNamedSBaseWithUnit() Initializes a new object of type AbstractNamedSBaseWithUnit whose identifier and name are set to null and whose level and version are set to -1 each.
AbstractNamedSBaseWithUnit(AbstractNamedSBaseWithUnit nsbu)
AbstractNamedSBaseWithUnit(int level, int version)
AbstractNamedSBaseWithUnit(java.lang.String id)
AbstractNamedSBaseWithUnit(java.lang.String id, int level, int version)
AbstractNamedSBaseWithUnit(java.lang.String id, java.lang.String name, int level, int version)

Method Summary

Modifier and Type	Method and Description
abstract AbstractNamedSBaseWithUnit	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	containsUndeclaredUnits() Returns true or false depending on whether this SBaseWithDerivedUnit refers to elements such as parameters or numbers with undeclared units.
boolean	equals(java.lang.Object object) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
UnitDefinition	getDerivedUnitDefinition() Derives the unit of this quantity and tries to identify an equivalent UnitDefinition within the corresponding Model.
java.lang.String	getDerivedUnits() Derives the unit of this quantity.
abstract java.lang.String	getPredefinedUnitID() Returns the predefined unit identifier for this data type with the current level/version combination.
java.lang.String	getUnits()
UnitDefinition	getUnitsInstance()
int	hashCode() Returns a hash code value for this SBase instance.
boolean	isPredefinedUnitsID(java.lang.String unitsID) Checks whether or not a given identifier for a Unit.Kind or UnitDefinition equals a predefined unit identifier for this type.
boolean	isSetUnits()
boolean	isSetUnitsInstance() Checks whether the element referenced by the unitsID attribute of this SBaseWithUnit is either an existing base Unit, i.e., a simple Unit that can directly be addressed via its Unit.Kind element, or the identifier of an existing UnitDefinition in the Model to which this SBaseWithUnit belongs.
void	setUnits(java.lang.String units) Sets the unitsID of this SBaseWithUnit.
void	setUnits(Unit.Kind unitKind) Sets the unit of this SBaseWithUnit.
void	setUnits(Unit unit) Sets the Unit of this SBaseWithUnit.
void	setUnits(UnitDefinition units) Set the unit attribute of this SBaseWithUnit to the given unit definition.
void	unsetUnits() Sets the unitsID of this SBaseWithUnit to null.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

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, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, 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, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setLevelAndVersion, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageNamespaceAndVersion, 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, 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.NamedSBase

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

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, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, readAttribute, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, 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, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

logger

private static final transient org.apache.log4j.Logger logger

Log4j logger

unitsID

protected java.lang.String unitsID

The unit attribute of this variable.

Constructor Detail

AbstractNamedSBaseWithUnit

public AbstractNamedSBaseWithUnit()

Initializes a new object of type AbstractNamedSBaseWithUnit whose identifier and name are set to null and whose level and version are set to -1 each.

AbstractNamedSBaseWithUnit

public AbstractNamedSBaseWithUnit(AbstractNamedSBaseWithUnit nsbu)

Parameters:

nsbu -

AbstractNamedSBaseWithUnit

public AbstractNamedSBaseWithUnit(int level,
                                  int version)

Parameters:

level -

version -

AbstractNamedSBaseWithUnit

public AbstractNamedSBaseWithUnit(java.lang.String id)

Parameters:

id -

AbstractNamedSBaseWithUnit

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

Parameters:

id -

level -

version -

AbstractNamedSBaseWithUnit

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

Parameters:

id -

name -

level -

version -

Method Detail

clone

public abstract AbstractNamedSBaseWithUnit 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

containsUndeclaredUnits

public boolean containsUndeclaredUnits()

Description copied from interface: SBaseWithDerivedUnit

Returns true or false depending on whether this SBaseWithDerivedUnit refers to elements such as parameters or numbers with undeclared units. A return value of true indicates that the UnitDefinition returned by SBaseWithDerivedUnit.getDerivedUnitDefinition() may not accurately represent the units of the expression.

Specified by:

containsUndeclaredUnits in interface SBaseWithDerivedUnit

Returns:

true if the math expression of this SBaseWithDerivedUnit includes parameters/numbers with undeclared units, false otherwise.

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 AbstractSBase

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.

getDerivedUnitDefinition

public UnitDefinition getDerivedUnitDefinition()

Description copied from interface: SBaseWithDerivedUnit

Derives the unit of this quantity and tries to identify an equivalent UnitDefinition within the corresponding Model. If no equivalent unit definition can be found, a new unit definition will be created that is not part of the model but represents the unit of this quantity. If it is not possible to derive a unit for this quantity, null will be returned.

Specified by:

getDerivedUnitDefinition in interface SBaseWithDerivedUnit

Returns:

a UnitDefinition that represent the derived unit of this quantity, or null if it is not possible to derive a unit.

getDerivedUnits

public java.lang.String getDerivedUnits()

Description copied from interface: SBaseWithDerivedUnit

Derives the unit of this quantity. If the model that contains this quantity already contains a unit that is equivalent to the derived unit, the corresponding identifier will be returned. In case that the unit cannot be derived or that no equivalent unit exists within the model, or if the model has not been defined yet, null will be returned. In case that this quantity represents a basic Unit.Kind this method will return the String representation of this Unit.Kind.

Specified by:

getDerivedUnits in interface SBaseWithDerivedUnit

Returns:

a String that represent the id of a UnitDefinition. This UnitDefinition represent the derived unit of this quantity. If it is not possible to derive a unit for this quantity or if no equivalent UnitDefinition can be found in the Model, null is returned.

getPredefinedUnitID

public abstract java.lang.String getPredefinedUnitID()

Returns the predefined unit identifier for this data type with the current level/version combination.

Returns:

an identifier of a unit in the containing Model. This can be one of the predefined unit identifiers if there are any.

getUnits

public java.lang.String getUnits()

Specified by:

getUnits in interface SBaseWithUnit

Returns:

the unitsID of this SBaseWithUnit. The empty String if it is not set.

getUnitsInstance

public UnitDefinition getUnitsInstance()

Specified by:

getUnitsInstance in interface SBaseWithUnit

Returns:

The UnitDefinition instance which has the unitsID of this SBaseWithUnit as id. Null if it doesn't exist. In case that the unit of this SBaseWithUnit represents a base Unit, a new UnitDefinition will be created and returned by this method. This new UnitDefinition will only contain the one unit represented by the unit identifier in this SBaseWithUnit. Note that the corresponding model will not contain this UnitDefinition. The identifier of this new UnitDefinition will be set to the same value as the name of the base Unit.

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 AbstractSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

isPredefinedUnitsID

public boolean isPredefinedUnitsID(java.lang.String unitsID)

Checks whether or not a given identifier for a Unit.Kind or UnitDefinition equals a predefined unit identifier for this type.

Parameters:

unitsID - the identifier to be checked.

Returns:

true if the given identifier equals the unit definition identifier that is predefined under the Level/Version combination for this data type.

isSetUnits

public boolean isSetUnits()

Specified by:

isSetUnits in interface SBaseWithUnit

Returns:

true if the unitsID of this element is not null.

isSetUnitsInstance

public boolean isSetUnitsInstance()

Description copied from interface: SBaseWithUnit

Checks whether the element referenced by the unitsID attribute of this SBaseWithUnit is either an existing base Unit, i.e., a simple Unit that can directly be addressed via its Unit.Kind element, or the identifier of an existing UnitDefinition in the Model to which this SBaseWithUnit belongs.

Specified by:

isSetUnitsInstance in interface SBaseWithUnit

Returns:

true if either a UnitDefinition, which has the unitsID of this SBaseWithUnit, can be found in the Model to which this SBaseWithUnit belongs, or if this element's unitsID as a corresponding base Unit for the given Level/Version combination.

setUnits

public void setUnits(Unit.Kind unitKind)

Description copied from interface: SBaseWithUnit

Sets the unit of this SBaseWithUnit. A new unit will be created base on this kind.

Specified by:

setUnits in interface SBaseWithUnit

setUnits

public void setUnits(java.lang.String units)

Description copied from interface: SBaseWithUnit

Sets the unitsID of this SBaseWithUnit. Only valid unit kind names or identifiers of already existing UnitDefinitions are allowed arguments of this function.

Specified by:

setUnits in interface SBaseWithUnit

Parameters:

units - the identifier of an already existing UnitDefinition or an Unit.Kind identifier for the current level/version combination of this unit. Passing a null value to this method is equivalent to calling SBaseWithUnit.unsetUnits().

setUnits

public void setUnits(Unit unit)

Description copied from interface: SBaseWithUnit

Sets the Unit of this SBaseWithUnit.

Specified by:

setUnits in interface SBaseWithUnit

setUnits

public void setUnits(UnitDefinition units)

Description copied from interface: SBaseWithUnit

Set the unit attribute of this SBaseWithUnit to the given unit definition.

Specified by:

setUnits in interface SBaseWithUnit

unsetUnits

public void unsetUnits()

Description copied from interface: SBaseWithUnit

Sets the unitsID of this SBaseWithUnit to null.

Specified by:

unsetUnits in interface SBaseWithUnit