Package org.sbml.jsbml

Class Symbol

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.AbstractNamedSBaseWithUnit

org.sbml.jsbml.QuantityWithUnit

org.sbml.jsbml.Symbol

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, CallableSBase, NamedSBase, NamedSBaseWithDerivedUnit, Quantity, SBase, SBaseWithDerivedUnit, SBaseWithUnit, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport, Variable

Direct Known Subclasses:

Compartment, Parameter, Species

public abstract class Symbol
extends QuantityWithUnit
implements Variable

The base class for Compartment, Species, Parameter. A symbol is a Variable of the system that declares a unit and a value, i.e., neither its Unit or UnitDefinition, nor its value are derived. A Symbol defines both fields. Furthermore, a Symbol may vary through a simulation and can be accessed within the model through its identifier and name attributes.

Since:

0.8

Author:

Andreas Dräger, Marine Dumousseau, Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

JSBML_WRONG_SBO_TERM

Constructor Summary

Constructors

Constructor	Description
Symbol()	Creates a Symbol instance.
Symbol(int level, int version)	Creates a Symbol instance from a level and version.
Symbol(java.lang.String id)	Creates a Symbol instance.
Symbol(java.lang.String id, int level, int version)	Creates a Symbol instance from an id, level and version.
Symbol(java.lang.String id, java.lang.String name, int level, int version)	Creates a Symbol instance from an id, name, level and version.
Symbol(QuantityWithUnit quantity)	Creates a Symbol instance.
Symbol(Symbol nsb)	Creates a Symbol instance from a given Symbol.

Method Summary

Modifier and Type	Method	Description
abstract Symbol	clone()	Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	equals(java.lang.Object o)	Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
boolean	getConstant()
int	hashCode()	Returns a hash code value for this SBase instance.
boolean	isConstant()
boolean	isSetConstant()
void	setConstant(boolean constant)	Sets the constant boolean of this Variable.
void	unsetConstant()	With this method the constant property of this variable will be set to an undefined state.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractNamedSBaseWithUnit

containsUndeclaredUnits, getDerivedUnitDefinition, getDerivedUnits, getPredefinedUnitID, getUnits, getUnitsInstance, isPredefinedUnitsID, isSetUnits, isSetUnitsInstance, setUnits, setUnits, setUnits, setUnits, unsetUnits

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, readAttribute, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, 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, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from interface org.sbml.jsbml.NamedSBase

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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.Quantity

getValue, isSetValue, setValue, unsetValue

Methods inherited from class org.sbml.jsbml.QuantityWithUnit

getValue, isIdMandatory, isSetValue, setValue, unsetValue

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, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, readAttribute, 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, writeXMLAttributes

Methods inherited from interface org.sbml.jsbml.SBaseWithDerivedUnit

containsUndeclaredUnits, getDerivedUnitDefinition, getDerivedUnits

Methods inherited from interface javax.swing.tree.TreeNode

children, getAllowsChildren, getChildAt, getChildCount, 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

Symbol

public Symbol()

Creates a Symbol instance. By default, value, unitsID, constant are null.

Symbol

public Symbol(int level,
              int version)

Creates a Symbol instance from a level and version. By default, value, unitsID, constant are null.

Parameters:

level - the SBML level

version - the SBML version

Symbol

public Symbol(QuantityWithUnit quantity)

Creates a Symbol instance.

Parameters:

quantity -

Symbol

public Symbol(java.lang.String id)

Creates a Symbol instance.

Parameters:

id -

Symbol

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

Creates a Symbol instance from an id, level and version. By default, value, unitsID, constant are null.

Parameters:

id -

level -

version -

Symbol

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

Creates a Symbol instance from an id, name, level and version. By default, value, unitsID, constant are null.

Parameters:

id -

name -

level -

version -

Symbol

public Symbol(Symbol nsb)

Creates a Symbol instance from a given Symbol.

Parameters:

nsb -

Method Detail

clone

public abstract Symbol 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 QuantityWithUnit

Returns:

a copy of this object

equals

public boolean equals(java.lang.Object o)

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 QuantityWithUnit

Parameters:

o - 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.

getConstant

public boolean getConstant()

Specified by:

getConstant in interface Variable

Returns:

the constant boolean of this variable.

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 QuantityWithUnit

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

isConstant

public boolean isConstant()

Specified by:

isConstant in interface Variable

Returns:

the constant value if it is set, false otherwise.

isSetConstant

public boolean isSetConstant()

Specified by:

isSetConstant in interface Variable

Returns:

true if the constant boolean of this Variable is not null.

setConstant

public void setConstant(boolean constant)

Description copied from interface: Variable

Sets the constant boolean of this Variable.

Specified by:

setConstant in interface Variable

unsetConstant

public void unsetConstant()

Description copied from interface: Variable

With this method the constant property of this variable will be set to an undefined state.

Specified by:

unsetConstant in interface Variable