org.sbml.jsbml

Class AssignmentRule

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractMathContainer

org.sbml.jsbml.Rule

org.sbml.jsbml.ExplicitRule

org.sbml.jsbml.AssignmentRule

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, Assignment, MathContainer, SBase, SBaseWithDerivedUnit, SBaseWithUnit, TreeNodeWithChangeSupport

public class AssignmentRule
extends ExplicitRule

Represents the assignmentRule XML element of a SBML file.

Since:

0.8

Version:

$Rev: 1639 $

Author:

Andreas Dräger, Marine Dumousseau

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private static long	serialVersionUID Generated serial version identifier.

Fields inherited from class org.sbml.jsbml.ExplicitRule

unitsID, variableID

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, lv

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Fields inherited from interface org.sbml.jsbml.Assignment

ILLEGAL_CONSTANT_VARIABLE_MSG, ILLEGAL_VARIABLE_EXCEPTION_MSG, NO_SUCH_VARIABLE_EXCEPTION_MSG

Constructor Summary

Constructors

Constructor and Description
AssignmentRule() Creates an AssignmentRule instance.
AssignmentRule(AssignmentRule ar) Creates a cloned AssignmentRule instance from a given AssignmentRule.
AssignmentRule(ASTNode math, int level, int version) Creates an AssignmentRule instance from a given math, level and version.
AssignmentRule(ASTNode math, Parameter parameter) Creates an AssignmentRule instance from a given math and Parameter.
AssignmentRule(ASTNode math, Variable variable) Creates an AssignmentRule instance from a given math and Variable.
AssignmentRule(ExplicitRule rule) Creates a cloned AssignmentRule instance from a given ExplicitRule.
AssignmentRule(int level, int version) Creates an AssignmentRule instance with the given level and version.
AssignmentRule(Parameter parameter) Creates an AssignmentRule instance from a given Parameter.
AssignmentRule(Parameter parameter, ASTNode math) Creates an AssignmentRule instance from a given math and Parameter.
AssignmentRule(Variable variable) Creates an AssignmentRule instance from a given variable.
AssignmentRule(Variable variable, ASTNode math) Creates an AssignmentRule instance from a given variable and math.

Method Summary

Methods

Modifier and Type	Method and Description
AssignmentRule	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
java.lang.String	getElementName() Returns the XML element name of this object.
boolean	isScalar() Predicate returning true or false depending on whether this Rule is an AssignmentRule (SBML Level 2) or has a 'type' attribute value of 'scalar' (SBML Level 1).

Methods inherited from class org.sbml.jsbml.ExplicitRule

equals, getUnits, getUnitsInstance, getVariable, getVariableInstance, hashCode, initDefaults, isCompartmentVolume, isParameter, isSetUnits, isSetUnitsInstance, isSetVariable, isSetVariableInstance, isSpeciesConcentration, readAttribute, setUnits, setUnits, setUnits, setUnits, setVariable, setVariable, unsetUnits, unsetVariable, writeXMLAttributes

Methods inherited from class org.sbml.jsbml.Rule

getParent, isAlgebraic, isAssignment, isRate

Methods inherited from class org.sbml.jsbml.AbstractMathContainer

containsUndeclaredUnits, getAllowsChildren, getChildAt, getChildCount, getDerivedUnitDefinition, getDerivedUnits, getFormula, getMath, getMathMLString, isSetMath, setFormula, setMath, toString, unsetFormula, unsetMath

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getExtension, 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, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, setAnnotation, setHistory, setLevel, setLevelAndVersion, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregister, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, firePropertyChange, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isRoot, isSetParent, isSetUserObjects, putUserObject, 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.MathContainer

getFormula, getMath, getMathMLString, isSetMath, setFormula, setMath, unsetFormula, unsetMath

Methods inherited from interface org.sbml.jsbml.SBaseWithDerivedUnit

containsUndeclaredUnits, getDerivedUnitDefinition, getDerivedUnits

Methods inherited from interface org.sbml.jsbml.SBase

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

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, 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

Constructor Detail

AssignmentRule

public AssignmentRule()

Creates an AssignmentRule instance. By default, the variableID is null.

AssignmentRule

public AssignmentRule(AssignmentRule ar)

Creates a cloned AssignmentRule instance from a given AssignmentRule.

Parameters:

ar - the AssignmentRule to clone.

AssignmentRule

public AssignmentRule(ExplicitRule rule)

Creates a cloned AssignmentRule instance from a given ExplicitRule.

Parameters:

rule - the AssignmentRule to clone.

AssignmentRule

public AssignmentRule(ASTNode math,
              int level,
              int version)

Creates an AssignmentRule instance from a given math, level and version.

Parameters:

math - the math

level - the SBML level

version - the SBML version

AssignmentRule

public AssignmentRule(ASTNode math,
              Parameter parameter)

Creates an AssignmentRule instance from a given math and Parameter.

Parameters:

math - the math

parameter - the parameter

AssignmentRule

public AssignmentRule(ASTNode math,
              Variable variable)

Creates an AssignmentRule instance from a given math and Variable.

Parameters:

math - the math

variable - the variable

AssignmentRule

public AssignmentRule(int level,
              int version)

Creates an AssignmentRule instance with the given level and version.

Parameters:

level - the SBML level

version - the SBML version

AssignmentRule

public AssignmentRule(Parameter parameter)

Creates an AssignmentRule instance from a given Parameter.

Parameters:

parameter - the parameter

AssignmentRule

public AssignmentRule(Parameter parameter,
              ASTNode math)

Creates an AssignmentRule instance from a given math and Parameter.

Parameters:

parameter - the parameter

math - the math

AssignmentRule

public AssignmentRule(Variable variable)

Creates an AssignmentRule instance from a given variable. Takes level and version from the variable.

Parameters:

variable - the Variable

AssignmentRule

public AssignmentRule(Variable variable,
              ASTNode math)

Creates an AssignmentRule instance from a given variable and math. Takes level and version from the variable.

Parameters:

variable - the Variable

math - the math

Method Detail

clone

public AssignmentRule 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 ExplicitRule

Returns:

a copy of this object

getElementName

public java.lang.String getElementName()

Description copied from interface: SBase

Returns the XML element name of this object.

Specified by:

getElementName in interface SBase

Overrides:

getElementName in class AbstractSBase

Returns:

the XML element name of this object.

isScalar

public boolean isScalar()

Description copied from class: ExplicitRule

Predicate returning true or false depending on whether this Rule is an AssignmentRule (SBML Level 2) or has a 'type' attribute value of 'scalar' (SBML Level 1).

Specified by:

isScalar in class ExplicitRule

Returns:

true if this Rule is an AssignmentRule (Level 2) or has type 'scalar' (Level 1), false otherwise.