Package 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, UniqueSId, 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

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
Parameter()	Creates a Parameter instance.
Parameter(int level, int version)	Creates a Parameter instance from a level and version.
Parameter(java.lang.String id)	Creates a Parameter instance from an id.
Parameter(java.lang.String id, int level, int version)	Creates a Parameter instance from an id, level and version.
Parameter(LocalParameter localParameter)	Creates a Parameter instance from a given LocalParameter.
Parameter(Parameter p)	Creates a Parameter instance from a given Parameter.

Method Summary

Modifier and Type	Method	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 Double.NaN value.
void	initDefaults(int level, int version, boolean explicit)
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)	Sets the given attribute in this SBase.
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.AbstractNamedSBase

isValidId

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.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, 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

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, 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

Methods inherited from interface org.sbml.jsbml.SBaseWithDerivedUnit

containsUndeclaredUnits, getDerivedUnitDefinition, getDerivedUnits

Methods inherited from class org.sbml.jsbml.Symbol

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

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

Parameter

public Parameter()

Creates a Parameter instance.

Parameter

public Parameter(int level,
                 int version)

Creates a Parameter instance from a level and version.

Parameters:

level - the SBML level

version - the SBML version

Parameter

public Parameter(LocalParameter localParameter)

Creates a Parameter instance from a given 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)

Creates a Parameter instance from an id.

Parameters:

id -

Parameter

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

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

Parameters:

id -

level - the SBML level

version - the SBML version

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 Double.NaN value.

Parameters:

level -

version -

initDefaults

public void initDefaults(int level,
                         int version,
                         boolean explicit)

Parameters:

level -

version -

explicit -

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

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.