org.sbml.jsbml

Class RateRule

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.RateRule

All Implemented Interfaces:

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

public class RateRule
extends ExplicitRule

Represents the rateRule XML element of a SBML file.

Since:

0.8

Version:

$Rev: 1966 $

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
RateRule() Creates a RateRule instance.
RateRule(ASTNode math, int level, int version) Creates a new RateRule instance.
RateRule(ASTNode math, Parameter parameter) Creates a new RateRule instance.
RateRule(ASTNode math, Variable variable) Creates a new RateRule instance.
RateRule(ExplicitRule rule) Creates a RateRule instance cloned from the given ExplicitRule
RateRule(int level, int version) Creates a RateRule instance from a given RateRule.
RateRule(Parameter parameter) Creates a new RateRule instance.
RateRule(Parameter parameter, ASTNode math) Creates a new RateRule instance.
RateRule(RateRule sb) Creates a new RateRule instance cloned from the given RateRule.
RateRule(Variable variable) Creates a RateRule instance from a given Symbol.
RateRule(Variable variable, ASTNode math) Creates a RateRule instance from a given Symbol and ASTNode.

Method Summary

Methods

Modifier and Type	Method and Description
RateRule	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
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, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, 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, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setLevelAndVersion, 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.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, 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

Constructor Detail

RateRule

public RateRule()

Creates a RateRule instance. By default, the variableID is null.

RateRule

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

Creates a new RateRule instance.

Parameters:

math - the ASTNode representing the mathematic formula of this rule.

level - the SBML level

version - the SBML version

RateRule

public RateRule(ASTNode math,
        Parameter parameter)

Creates a new RateRule instance.

Parameters:

math -

parameter -

RateRule

public RateRule(ASTNode math,
        Variable variable)

Creates a new RateRule instance.

Parameters:

variable -

math -

RateRule

public RateRule(int level,
        int version)

Creates a RateRule instance from a given RateRule.

Parameters:

level - the SBML level

version - the SBML version

RateRule

public RateRule(Parameter parameter)

Creates a new RateRule instance.

Parameters:

parameter -

RateRule

public RateRule(Parameter parameter,
        ASTNode math)

Creates a new RateRule instance.

Parameters:

parameter -

math -

RateRule

public RateRule(RateRule sb)

Creates a new RateRule instance cloned from the given RateRule.

Parameters:

sb -

RateRule

public RateRule(Variable variable)

Creates a RateRule instance from a given Symbol. Takes level and version from the variable.

Parameters:

variable -

RateRule

public RateRule(ExplicitRule rule)

Creates a RateRule instance cloned from the given ExplicitRule

Parameters:

rule -

RateRule

public RateRule(Variable variable,
        ASTNode math)

Creates a RateRule instance from a given Symbol and ASTNode. Takes level and version from the variable.

Parameters:

variable -

math -

Method Detail

clone

public RateRule 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

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.