java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, NamedSBase
, SBase
, TreeNodeWithChangeSupport
public class Uncertainty extends AbstractDistribSBase
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.
JSBML_WRONG_SBO_TERM
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
|
Modifier and Type | Method | Description |
---|---|---|
boolean |
addUncertParameter(UncertParameter uncertParameter) |
Adds a new
UncertParameter to the listOfUncertParameters . |
Uncertainty |
clone() |
Creates a deep copy of this object, i.e., a new
SBase with the same
properties
like this one. |
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
UncertParameter s 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
UncertParameter s in this
Uncertainty . |
void |
initDefaults() |
Initializes the default values using the namespace.
|
boolean |
isIdMandatory() |
Returns
true if the identifier of this
SBase is required to be defined (i.e., not null )
in the definition of SBML. |
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() |
getPackageName, writeXMLAttributes
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, 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, 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, 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
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
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName
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
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
public Uncertainty()
public Uncertainty(java.lang.String id)
id
- the identifier for the new element.public Uncertainty(int level, int version)
level
- SBML Levelversion
- SBML Versionpublic Uncertainty(java.lang.String id, int level, int version)
id
- the identifier for this element.level
- the SBML Levelversion
- the SBML Versionpublic Uncertainty(java.lang.String id, java.lang.String name, int level, int version)
id
- the identifier for this element.name
- a human-readable name for this element that can be used for display purposes.level
- the SBML Levelversion
- the SBML Versionpublic Uncertainty(Uncertainty obj)
obj
- the object to clonepublic void initDefaults()
public boolean isIdMandatory()
SBase
true
if the identifier of this
SBase
is required to be defined (i.e., not null
)
in the definition of SBML.isIdMandatory
in interface NamedSBase
isIdMandatory
in interface SBase
isIdMandatory
in class AbstractSBase
true
if the identifier of this element must be set in
order to create a valid SBML representation. false
otherwise, i.e., if the identifier can be understood as an optional
attribute.public Uncertainty clone()
SBase
SBase
with the same
properties
like this one.clone
in interface SBase
clone
in class AbstractSBase
public boolean getAllowsChildren()
getAllowsChildren
in interface javax.swing.tree.TreeNode
getAllowsChildren
in class AbstractDistribSBase
public int getChildCount()
getChildCount
in interface javax.swing.tree.TreeNode
getChildCount
in class AbstractDistribSBase
public javax.swing.tree.TreeNode getChildAt(int index)
getChildAt
in interface javax.swing.tree.TreeNode
getChildAt
in class AbstractDistribSBase
public boolean isSetListOfUncertParameters()
true
if listOfUncertParameters
contains at least
one element.true
if listOfUncertParameters
contains at least
one element, otherwise false
.public ListOf<UncertParameter> getListOfUncertParameters()
listOfUncertParameters
.
Creates it if it does not already exist.listOfUncertParameters
.public void setListOfUncertParameters(ListOf<UncertParameter> listOfUncertParameters)
ListOf<UncertParameter>
.
If listOfUncertParameters
was defined before and contains some
elements, they are all unset.listOfUncertParameters
- public boolean unsetListOfUncertParameters()
true
if listOfUncertParameters
contains at least
one element, otherwise false
.public boolean addUncertParameter(UncertParameter uncertParameter)
UncertParameter
to the listOfUncertParameters
.
The listOfUncertParameters is initialized if necessary.
uncertParameter
- the element to add to the listtrue
(as specified by Collection.add(E)
)Collection.add(Object)
public boolean removeUncertParameter(UncertParameter uncertParameter)
listOfUncertParameters
.uncertParameter
- the element to be removed from the list.true
if the list contained the specified element and it was
removed.List.remove(Object)
public UncertParameter removeUncertParameter(java.lang.String uncertParameterId)
listOfUncertParameters
.uncertParameterId
- the id of the element to be removed from the list.null
.public UncertParameter removeUncertParameter(int i)
listOfUncertParameters
at the given index.i
- the index where to remove the UncertParameter
.java.lang.IndexOutOfBoundsException
- if the listOf is not set or if the index is
out of bound ((i < 0) || (i > listOfUncertParameters)
).public UncertParameter createUncertParameter()
listOfUncertParameters
list.listOfUncertParameters
public UncertParameter createUncertParameter(java.lang.String id)
UncertParameter
element and adds it to the
listOfUncertParameters
list.id
- the identifier that is to be applied to the new element.UncertParameter
element, which is the last
element in the listOfUncertParameters
.public UncertSpan createUncertSpan()
UncertSpan
element and adds it to the
listOfUncertParameters
list.listOfUncertParameters
public UncertSpan createUncertSpan(java.lang.String id)
UncertSpan
element and adds it to the
listOfUncertParameters
list.id
- the identifier that is to be applied to the new element.listOfUncertParameters
public UncertParameter getUncertParameter(int i)
listOfUncertParameters
at the given index.i
- the index of the UncertParameter
element to get.java.lang.IndexOutOfBoundsException
- if the listOf is not set or
if the index is out of bound (index < 0 || index > list.size).public UncertParameter getUncertParameter(java.lang.String uncertParameterId)
uncertParameterId
- the id of the UncertParameter
element to get.null
.public int getUncertParameterCount()
UncertParameter
s in this
Uncertainty
.UncertParameter
s in this
Uncertainty
.public int getNumUncertParameters()
UncertParameter
s in this
Uncertainty
.UncertParameter
s in this
Uncertainty
.getUncertParameterCount()