Package org.sbml.jsbml.ext.distrib

Class UncertSpan

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.distrib.AbstractDistribSBase

org.sbml.jsbml.ext.distrib.UncertParameter

org.sbml.jsbml.ext.distrib.UncertSpan

All Implemented Interfaces:

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

public class UncertSpan
extends UncertParameter

The UncertSpan class defines a span of values that define an uncertainty statistic such as confidence interval or range.

It inherits from UncertParameter, and adds four optional attributes, varLower and varUpper, of type String, and valueLower and valueUpper, of type double. Exactly one of the attributes varLower and valueLower may be defined, and exactly one of the attributes varUpper and valueUpper may be defined. If no attributes are defined, the parameters of the span are undefined. If only one attribute is defined (one of the upper or lower attributes), that aspect of the span is defined, and the other end is undefined. The span is fully defined if two attributes (one lower and one upper) are defined.

The value of the lower attribute (whichever is defined) must be lesser or equal to the value of the upper attribute (whichever is defined), at the initial conditions of the model. The Uncertainty element cannot affect the core mathematics of an SBML model, but if it is used in a mathematical context during simulation of the model, this restriction on the attribute values must be maintained, or the UncertSpan object as a whole will be undefined. Like the units attribute on an UncertParameter , the units attribute is provided if valueUpper and/or valueLower is defined. The units on both the upper and lower ends of the span must match each other, if defined. The units for span ends defined by reference may be obtained from the referenced SBML element.

Since:

1.5

Author:

rodrigue

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.sbml.jsbml.ext.distrib.UncertParameter

UncertParameter.Type

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

Method Summary

Modifier and Type	Method	Description
UncertSpan	clone()	clones this class
boolean	equals(java.lang.Object obj)
double	getValueLower()	Returns the value of valueLower.
double	getValueUpper()	Returns the value of valueUpper.
java.lang.String	getVarLower()	Returns the value of varLower.
java.lang.String	getVarUpper()	Returns the value of varUpper.
int	hashCode()
void	initDefaults()	Initializes the default values using the namespace.
boolean	isSetValueLower()	Returns whether valueLower is set.
boolean	isSetValueUpper()	Returns whether valueUpper is set.
boolean	isSetVarLower()	Returns whether varLower is set.
boolean	isSetVarUpper()	Returns whether varUpper is set.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
void	setValueLower(double valueLower)	Sets the value of valueLower
void	setValueUpper(double valueUpper)	Sets the value of valueUpper
void	setVarLower(java.lang.String varLower)	Sets the value of varLower
void	setVarUpper(java.lang.String varUpper)	Sets the value of varUpper
boolean	unsetValueLower()	Unsets the variable valueLower.
boolean	unsetValueUpper()	Unsets the variable valueUpper.
boolean	unsetVarLower()	Unsets the variable varLower.
boolean	unsetVarUpper()	Unsets the variable varUpper.
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes()

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

getPackageName

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, 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, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, 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, isIdMandatory, 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, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, 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

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

addUncertParameter, containsUndeclaredUnits, createUncertParameter, createUncertParameter, getAllowsChildren, getChildAt, getChildCount, getDefinitionURL, getDerivedUnitDefinition, getDerivedUnits, getFormula, getListOfUncertParameters, getMath, getMathMLString, getNumUncertParameters, getType, getUncertParameter, getUncertParameter, getUncertParameterCount, getUnits, getValue, getVar, isSetDefinitionURL, isSetListOfUncertParameters, isSetMath, isSetType, isSetUnits, isSetValue, isSetVar, removeUncertParameter, removeUncertParameter, removeUncertParameter, setDefinitionURL, setFormula, setListOfUncertParameters, setMath, setType, setUnits, setValue, setVar, unsetDefinitionURL, unsetFormula, unsetListOfUncertParameters, unsetMath, unsetType, unsetUnits, unsetValue, unsetVar

Constructor Detail

UncertSpan

public UncertSpan()

Creates an UncertSpan instance

UncertSpan

public UncertSpan(java.lang.String id)

Creates a UncertSpan instance with an id.

Parameters:

id - the identifier for the new element.

UncertSpan

public UncertSpan(int level,
                  int version)

Creates a UncertSpan instance with a level and version.

Parameters:

level - SBML Level

version - SBML Version

UncertSpan

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

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

Parameters:

id - the identifier for this element.

level - the SBML Level

version - the SBML Version

UncertSpan

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

Creates a UncertSpan 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

UncertSpan

public UncertSpan(UncertSpan obj)

Clone constructor

Method Detail

clone

public UncertSpan clone()

clones this class

Specified by:

clone in interface SBase

Overrides:

clone in class UncertParameter

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

Overrides:

initDefaults in class UncertParameter

getValueLower

public double getValueLower()

Returns the value of valueLower.

Returns:

the value of valueLower.

isSetValueLower

public boolean isSetValueLower()

Returns whether valueLower is set.

Returns:

whether valueLower is set.

setValueLower

public void setValueLower(double valueLower)

Sets the value of valueLower

Parameters:

valueLower - the value of valueLower to be set.

unsetValueLower

public boolean unsetValueLower()

Unsets the variable valueLower.

Returns:

true if valueLower was set before, otherwise false.

getValueUpper

public double getValueUpper()

Returns the value of valueUpper.

Returns:

the value of valueUpper.

isSetValueUpper

public boolean isSetValueUpper()

Returns whether valueUpper is set.

Returns:

whether valueUpper is set.

setValueUpper

public void setValueUpper(double valueUpper)

Sets the value of valueUpper

Parameters:

valueUpper - the value of valueUpper to be set.

unsetValueUpper

public boolean unsetValueUpper()

Unsets the variable valueUpper.

Returns:

true if valueUpper was set before, otherwise false.

getVarLower

public java.lang.String getVarLower()

Returns the value of varLower.

Returns:

the value of varLower.

isSetVarLower

public boolean isSetVarLower()

Returns whether varLower is set.

Returns:

whether varLower is set.

setVarLower

public void setVarLower(java.lang.String varLower)

Sets the value of varLower

Parameters:

varLower - the value of varLower to be set.

unsetVarLower

public boolean unsetVarLower()

Unsets the variable varLower.

Returns:

true if varLower was set before, otherwise false.

getVarUpper

public java.lang.String getVarUpper()

Returns the value of varUpper.

Returns:

the value of varUpper.

isSetVarUpper

public boolean isSetVarUpper()

Returns whether varUpper is set.

Returns:

whether varUpper is set.

setVarUpper

public void setVarUpper(java.lang.String varUpper)

Sets the value of varUpper

Parameters:

varUpper - the value of varUpper to be set.

unsetVarUpper

public boolean unsetVarUpper()

Unsets the variable varUpper.

Returns:

true if varUpper was set before, otherwise false.

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class UncertParameter

equals

public boolean equals(java.lang.Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class UncertParameter

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class UncertParameter

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class UncertParameter