Package org.sbml.jsbml.ext.distrib

Class Uncertainty

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.distrib.AbstractDistribSBase

org.sbml.jsbml.ext.distrib.Uncertainty

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, SBase, org.sbml.jsbml.util.TreeNodeWithChangeSupport

public class Uncertainty
extends AbstractDistribSBase

The Uncertainty class is a collection of zero or more statistical measures related to the uncertainty of the parent SBML element.

It may only contain one of each type of measurement, which means that each of its UncertParameter children must have a unique type attribute for every value but 'externalParameter'. Each UncertParameter child with a type of 'externalParameter' must, in turn, have a unique definitionURL value. If a given SBML element has multiple measures of the same type (for example, as measured from different sources or different experiments), it should be given multiple Uncertainty children. Each Uncertainty child must be a unique set of statistical measures.

Note that the described uncertainty for elements that change in value over time apply only to the element's uncertainty at a snapshot in time, and not the uncertainty in how it changes in time. For typical simulations, this means the element's initial condition.

Since:

1.4

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
Uncertainty()	Creates an Uncertainty instance
Uncertainty(int level, int version)	Creates a Uncertainty instance with a level and version.
Uncertainty(java.lang.String id)	Creates a Uncertainty instance with an id.
Uncertainty(java.lang.String id, int level, int version)	Creates a Uncertainty instance with an id, level, and version.
Uncertainty(java.lang.String id, java.lang.String name, int level, int version)	Creates a Uncertainty instance with an id, name, level, and version.
Uncertainty(Uncertainty obj)	Clone constructor

Method Summary

Modifier and Type	Method	Description
boolean	addUncertParameter(UncertParameter uncertParameter)	Adds a new UncertParameter to the listOfUncertParameters.
Uncertainty	clone()
UncertParameter	createUncertParameter()	Creates a new UncertParameter element and adds it to the listOfUncertParameters list.
UncertParameter	createUncertParameter(java.lang.String id)	Creates a new UncertParameter element and adds it to the listOfUncertParameters list.
UncertSpan	createUncertSpan()	Creates a new UncertSpan element and adds it to the listOfUncertParameters list.
UncertSpan	createUncertSpan(java.lang.String id)	Creates a new UncertSpan element and adds it to the listOfUncertParameters list.
boolean	getAllowsChildren()
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
ListOf<UncertParameter>	getListOfUncertParameters()	Returns the listOfUncertParameters.
int	getNumUncertParameters()	Returns the number of UncertParameters in this Uncertainty.
UncertParameter	getUncertParameter(int i)	Gets an element from the listOfUncertParameters at the given index.
UncertParameter	getUncertParameter(java.lang.String uncertParameterId)	Gets an element from the listOfUncertParameters, with the given id.
int	getUncertParameterCount()	Returns the number of UncertParameters in this Uncertainty.
void	initDefaults()	Initializes the default values using the namespace.
boolean	isIdMandatory()
boolean	isSetListOfUncertParameters()	Returns true if listOfUncertParameters contains at least one element.
UncertParameter	removeUncertParameter(int i)	Removes an element from the listOfUncertParameters at the given index.
UncertParameter	removeUncertParameter(java.lang.String uncertParameterId)	Removes an element from the listOfUncertParameters.
boolean	removeUncertParameter(UncertParameter uncertParameter)	Removes an element from the listOfUncertParameters.
void	setListOfUncertParameters(ListOf<UncertParameter> listOfUncertParameters)	Sets the given ListOf<UncertParameter>.
boolean	unsetListOfUncertParameters()	Returns true if listOfUncertParameters contains at least one element, otherwise false.

Methods inherited from class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

getPackageName, 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, equals, 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, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, readAttribute, 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 interface org.sbml.jsbml.NamedSBase

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

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, equals, 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, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hashCode, 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

Methods inherited from interface javax.swing.tree.TreeNode

children, 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

Uncertainty

public Uncertainty()

Creates an Uncertainty instance

Uncertainty

public Uncertainty(java.lang.String id)

Creates a Uncertainty instance with an id.

Parameters:

id - the identifier for the new element.

Uncertainty

public Uncertainty(int level,
                   int version)

Creates a Uncertainty instance with a level and version.

Parameters:

level - SBML Level

version - SBML Version

Uncertainty

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

Creates a Uncertainty instance with an id, level, and version.

Parameters:

id - the identifier for this element.

level - the SBML Level

version - the SBML Version

Uncertainty

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

Creates a Uncertainty instance with an id, name, level, and version.

Parameters:

id - the identifier for this element.

name - a human-readable name for this element that can be used for display purposes.

level - the SBML Level

version - the SBML Version

Uncertainty

public Uncertainty(Uncertainty obj)

Clone constructor

Parameters:

obj - the object to clone

Method Detail

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

clone

public Uncertainty clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

Overrides:

getAllowsChildren in class AbstractDistribSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class AbstractDistribSBase

getChildAt

public javax.swing.tree.TreeNode getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractDistribSBase

isSetListOfUncertParameters

public boolean isSetListOfUncertParameters()

Returns true if listOfUncertParameters contains at least one element.

Returns:

true if listOfUncertParameters contains at least one element, otherwise false.

getListOfUncertParameters

public ListOf<UncertParameter> getListOfUncertParameters()

Returns the listOfUncertParameters. Creates it if it does not already exist.

Returns:

the listOfUncertParameters.

setListOfUncertParameters

public void setListOfUncertParameters(ListOf<UncertParameter> listOfUncertParameters)

Sets the given ListOf<UncertParameter>. If listOfUncertParameters was defined before and contains some elements, they are all unset.

Parameters:

listOfUncertParameters -

unsetListOfUncertParameters

public boolean unsetListOfUncertParameters()

Returns true if listOfUncertParameters contains at least one element, otherwise false.

Returns:

true if listOfUncertParameters contains at least one element, otherwise false.

addUncertParameter

public boolean addUncertParameter(UncertParameter uncertParameter)

Adds a new UncertParameter to the listOfUncertParameters.

The listOfUncertParameters is initialized if necessary.

Parameters:

uncertParameter - the element to add to the list

Returns:

true (as specified by Collection.add(E))

See Also:

Collection.add(Object)

removeUncertParameter

public boolean removeUncertParameter(UncertParameter uncertParameter)

Removes an element from the listOfUncertParameters.

Parameters:

uncertParameter - the element to be removed from the list.

Returns:

true if the list contained the specified element and it was removed.

See Also:

List.remove(Object)

removeUncertParameter

public UncertParameter removeUncertParameter(java.lang.String uncertParameterId)

Removes an element from the listOfUncertParameters.

Parameters:

uncertParameterId - the id of the element to be removed from the list.

Returns:

the removed element, if it was successfully found and removed or null.

removeUncertParameter

public UncertParameter removeUncertParameter(int i)

Removes an element from the listOfUncertParameters at the given index.

Parameters:

i - the index where to remove the UncertParameter.

Returns:

the specified element if it was successfully found and removed.

Throws:

java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound ((i < 0) || (i > listOfUncertParameters)).

createUncertParameter

public UncertParameter createUncertParameter()

Creates a new UncertParameter element and adds it to the listOfUncertParameters list.

Returns:

the newly created element, i.e., the last item in the listOfUncertParameters

createUncertParameter

public UncertParameter createUncertParameter(java.lang.String id)

Creates a new UncertParameter element and adds it to the listOfUncertParameters list.

Parameters:

id - the identifier that is to be applied to the new element.

Returns:

the newly created UncertParameter element, which is the last element in the listOfUncertParameters.

createUncertSpan

public UncertSpan createUncertSpan()

Creates a new UncertSpan element and adds it to the listOfUncertParameters list.

Returns:

the newly created element, i.e., the last item in the listOfUncertParameters

createUncertSpan

public UncertSpan createUncertSpan(java.lang.String id)

Creates a new UncertSpan element and adds it to the listOfUncertParameters list.

Parameters:

id - the identifier that is to be applied to the new element.

Returns:

the newly created element, i.e., the last item in the listOfUncertParameters

getUncertParameter

public UncertParameter getUncertParameter(int i)

Gets an element from the listOfUncertParameters at the given index.

Parameters:

i - the index of the UncertParameter element to get.

Returns:

an element from the listOfUncertParameters at the given index.

Throws:

java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).

getUncertParameter

public UncertParameter getUncertParameter(java.lang.String uncertParameterId)

Gets an element from the listOfUncertParameters, with the given id.

Parameters:

uncertParameterId - the id of the UncertParameter element to get.

Returns:

an element from the listOfUncertParameters with the given id or null.

getUncertParameterCount

public int getUncertParameterCount()

Returns the number of UncertParameters in this Uncertainty.

Returns:

the number of UncertParameters in this Uncertainty.

getNumUncertParameters

public int getNumUncertParameters()

Returns the number of UncertParameters in this Uncertainty.

Returns:

the number of UncertParameters in this Uncertainty.

Note: this method is kept here as it exist in libSBML.

same as getUncertParameterCount()