org.sbml.jsbml.ext.req

Class ChangedMath

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.req.ChangedMath

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, SBase, TreeNodeWithChangeSupport

public class ChangedMath
extends AbstractNamedSBase

Declares which package has modified the value or the mathematical meaning of an SBase and in which way.

Elements with mathematical meaning may have a ChangedMath child when a package alters the value or meaning of that symbol. As an example, a Submodel from the Hierarchical Model Composition package may contain an Event or Rule that assigns new values to a parameter. Because an interpreter that did not understand submodels would not catch this change, the Hierarchical Model Composition package can be seen to change the math of that element, and it would be appropriate to denote this by adding a ChangedMath child to the affected parameter.

Similarly, models that use the proposed Spatial Processes package can change the meaning of a Compartment by turning it into a bounded object with an size implied by those boundaries (and how they change over time), instead of using the element's size attribute. Spatial Processes elements may also change a Species to be spatially defined, and therefore represent different values depending on what coordinates in space are under consideration. Affected compartments and species could be given ChangedMath children to denote this fact.

Elements with Math children may also be changed by the addition of package elements. Some packages may instruct the modeler to disregard the Math and to use some other construct instead. For example, the proposed Distributions package adds a new child to FunctionDefinition, which replaces the old mathematics with a new set of mathematics returning a draw from a random distribution (something impossible with Math).

Since:

1.0

Version:

$Rev: 1686 $

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	changedBy The changedBy attribute is required, and is of type string.
private static long	serialVersionUID Generated serial version identifier.
private java.lang.Boolean	viableWithoutChange The viableWithoutChange attribute is required, and is of type boolean.

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
ChangedMath	clone() clones this class
java.lang.String	getChangedBy() Returns the value of changedBy
boolean	getViableWithoutChange() Returns the value of viableWithoutChange
void	initDefaults() Initializes the default values using the namespace.
boolean	isIdMandatory() This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.
boolean	isSetChangedBy() Returns whether changedBy is set
boolean	isSetViableWithoutChange() Returns whether viableWithoutChange is set
boolean	isViableWithoutChange() Returns the value of viableWithoutChange
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setChangedBy(java.lang.String changedBy) Sets the value of changedBy
void	setViableWithoutChange(boolean viableWithoutChange) Sets the value of viableWithoutChange
boolean	unsetChangedBy() Unsets the variable changedBy
boolean	unsetViableWithoutChange() Unsets the variable viableWithoutChange
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

equals, getId, getName, hashCode, isSetId, isSetName, isValidId, setId, setName, toString, unsetId, unsetName

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, 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, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, 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 class java.lang.Object

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

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, 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, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

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 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

viableWithoutChange

private java.lang.Boolean viableWithoutChange

The viableWithoutChange attribute is required, and is of type boolean. The attribute should be used to indicate whether an interpreter that does not understand the package from the changedBy attribute would have an interpretable version of the mathematics for the given component in a model. This can be established using two criteria: “Complete” and “Workable”. Obviously, if the math being interpreted is incomplete, the viableWithoutChange attribute must be false. If the math is complete, then whether the solution is “workable” requires a judgment call on the part of the modeler: if the modeler feels that the alternative version makes sense in an alternative context, they may set the attribute value to true; conversely, if they feel that the resulting model component makes no sense, even if technically “complete”, then they should set the attribute value to false.

changedBy

private java.lang.String changedBy

The changedBy attribute is required, and is of type string. The attribute must be set to the namespace URI of the SBML Level 3 package that redefines or alters the mathematical semantics of the parent object. In other words, if the mathematical semantics of a given component C in a model is changed by the use of a Level 3 package P, then C can be given a ChangedMath child, and its attribute changedBy should be P's namespace URI.

Constructor Detail

ChangedMath

public ChangedMath()

Creates an ChangedMath instance

ChangedMath

public ChangedMath(java.lang.String id)

Creates a ChangedMath instance with an id.

Parameters:

id -

ChangedMath

public ChangedMath(int level,
           int version)

Creates a ChangedMath instance with a level and version.

Parameters:

level -

version -

ChangedMath

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

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

Parameters:

id -

level -

version -

ChangedMath

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

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

Parameters:

id -

name -

level -

version -

ChangedMath

public ChangedMath(ChangedMath obj)

Clone constructor

Method Detail

clone

public ChangedMath clone()

clones this class

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

Returns:

a copy of this object

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: NamedSBase

This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.

Returns:

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.

getChangedBy

public java.lang.String getChangedBy()

Returns the value of changedBy

Returns:

the value of changedBy

isSetChangedBy

public boolean isSetChangedBy()

Returns whether changedBy is set

Returns:

whether changedBy is set

setChangedBy

public void setChangedBy(java.lang.String changedBy)

Sets the value of changedBy

unsetChangedBy

public boolean unsetChangedBy()

Unsets the variable changedBy

Returns:

true, if changedBy was set before, otherwise false

getViableWithoutChange

public boolean getViableWithoutChange()

Returns the value of viableWithoutChange

Returns:

the value of viableWithoutChange

Throws:

PropertyUndefinedError - - if the returned value of isSetViableWithoutChange() is false

isViableWithoutChange

public boolean isViableWithoutChange()

Returns the value of viableWithoutChange

Returns:

the value of viableWithoutChange

Throws:

PropertyUndefinedError - - if the returned value of isSetViableWithoutChange() is false

isSetViableWithoutChange

public boolean isSetViableWithoutChange()

Returns whether viableWithoutChange is set

Returns:

whether viableWithoutChange is set

setViableWithoutChange

public void setViableWithoutChange(boolean viableWithoutChange)

Sets the value of viableWithoutChange

unsetViableWithoutChange

public boolean unsetViableWithoutChange()

Unsets the variable viableWithoutChange

Returns:

true, if viableWithoutChange was set before, otherwise false

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 AbstractNamedSBase

Returns:

a Map containing the XML attributes of this object.

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 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.