org.sbml.jsbml

Class Parameter

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

org.sbml.jsbml.Parameter

All Implemented Interfaces:

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

public class Parameter
extends Symbol

Represents a globally valid parameter in the model, i.e., a variable that may change during a simulation or that provides a constant value.

Since:

0.8

Version:

$Rev: 1639 $

Author:

Andreas Dräger, Marine Dumousseau, Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private static long	serialVersionUID Generated serial version identifier.

Fields inherited from class org.sbml.jsbml.Symbol

constant, isSetConstant

Fields inherited from class org.sbml.jsbml.QuantityWithUnit

value

Fields inherited from class org.sbml.jsbml.AbstractNamedSBaseWithUnit

unitsID

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, lv

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
Parameter() Creates a Parameter instance.
Parameter(int level, int version) Creates a Parameter instance from an id, level and version.
Parameter(LocalParameter localParameter) This constructor allows the creation of a global Parameter based on a LocalParameter.
Parameter(Parameter p) Creates a Parameter instance from a given Parameter.
Parameter(java.lang.String id)
Parameter(java.lang.String id, int level, int version)

Method Summary

Methods

Modifier and Type	Method and Description
Parameter	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
java.lang.String	getPredefinedUnitID() Returns the predefined unit identifier for this data type with the current level/version combination.
void	initDefaults() Initializes the default values using the current Level/Version configuration.
void	initDefaults(int level, int version) Initializes the default values of this Parameter, i.e., sets it to a constant variable with a NaN value.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) If the attribute is an id or name attribute, it will set the id or name of this object with the value of the XML attribute ('value').
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.Symbol

equals, getConstant, hashCode, isConstant, isSetConstant, setConstant, unsetConstant

Methods inherited from class org.sbml.jsbml.QuantityWithUnit

getValue, isIdMandatory, isSetValue, setValue, unsetValue

Methods inherited from class org.sbml.jsbml.AbstractNamedSBaseWithUnit

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

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

checkIdentifier, getId, getName, isSetId, isSetName, isValidId, setId, setName, toString, unsetId, unsetName

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, setAnnotation, setHistory, setLevel, setLevelAndVersion, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregister, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, firePropertyChange, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isRoot, isSetParent, isSetUserObjects, putUserObject, 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.Quantity

getValue, isSetValue, setValue, unsetValue

Methods inherited from interface org.sbml.jsbml.NamedSBase

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

Methods inherited from interface org.sbml.jsbml.SBaseWithDerivedUnit

containsUndeclaredUnits, getDerivedUnitDefinition, getDerivedUnits

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregister, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

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

addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, 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

Generated serial version identifier.

See Also:

Constant Field Values

Constructor Detail

Parameter

public Parameter()

Creates a Parameter instance.

Parameter

public Parameter(int level,
         int version)

Creates a Parameter instance from an id, level and version.

Parameters:

id -

level -

version -

Parameter

public Parameter(LocalParameter localParameter)

This constructor allows the creation of a global Parameter based on a LocalParameter. It creates a new Parameter object that will have the same attributes than the LocalParameter. Its constant attribute will be set to true.

Parameters:

localParameter -

Parameter

public Parameter(Parameter p)

Creates a Parameter instance from a given Parameter.

Parameters:

p -

Parameter

public Parameter(java.lang.String id)

Parameters:

id -

Parameter

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

Parameters:

id -

Method Detail

clone

public Parameter 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 Symbol

Returns:

a copy of this object

getPredefinedUnitID

public java.lang.String getPredefinedUnitID()

Description copied from class: AbstractNamedSBaseWithUnit

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

Specified by:

getPredefinedUnitID in class AbstractNamedSBaseWithUnit

Returns:

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

initDefaults

public void initDefaults(int level,
                int version)

Initializes the default values of this Parameter, i.e., sets it to a constant variable with a NaN value.

initDefaults

public void initDefaults()

Initializes the default values using the current Level/Version configuration.

readAttribute

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

Description copied from interface: SBase

If the attribute is an id or name attribute, it will set the id or name of this object with the value of the XML attribute ('value').

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractNamedSBase

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()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractNamedSBase

Returns:

a Map containing the XML attributes of this object.