org.sbml.jsbml

Class ExplicitRule

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractMathContainer

org.sbml.jsbml.Rule

org.sbml.jsbml.ExplicitRule

All Implemented Interfaces:

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

Direct Known Subclasses:

AssignmentRule, RateRule, SBMLLevel1Rule

public abstract class ExplicitRule
extends Rule
implements Assignment, SBaseWithUnit

An explicit Rule is a rule that explicitly declares its variable element. Hence, this class provides methods to access and manipulate the variable field of the underlying Rule.

Since:

0.8

Version:

$Rev$

Author:

Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private static long	serialVersionUID Generated serial version identifier.
protected java.lang.String	unitsID Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
(package private) java.lang.String	variableID Represents the id of a Variable.

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, lv, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
ExplicitRule() Creates a new ExplicitRule.
ExplicitRule(ASTNode math, int level, int version) Creates a new ExplicitRule
ExplicitRule(ASTNode math, Variable variable) Creates a new ExplicitRule with the given ASTNode element for the assignment to the given Variable or the derivative of the Variable.
ExplicitRule(ExplicitRule rule) Creates a new ExplicitRule
ExplicitRule(int level, int version) Creates a new ExplicitRule
ExplicitRule(Parameter parameter) Creates a new ExplicitRule
ExplicitRule(Parameter parameter, ASTNode math) Creates a new ExplicitRule
ExplicitRule(Variable variable) Creates an ExplicitRule instance from a given Variable.
ExplicitRule(Variable variable, ASTNode math) Creates a new ExplicitRule

Method Summary

Modifier and Type	Method and Description
abstract ExplicitRule	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	equals(java.lang.Object object) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
java.lang.String	getUnits() Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
UnitDefinition	getUnitsInstance() Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
java.lang.String	getVariable() Returns the variableID of this Assignment.
Variable	getVariableInstance() Returns the Variable instance which has the variableID of this Assignment as id.
int	hashCode() Returns a hash code value for this SBase instance.
void	initDefaults()
boolean	isCompartmentVolume() (SBML Level 1 only) Predicate returning true or false depending on whether this Rule is an CompartmentVolumeRule.
boolean	isParameter() (SBML Level 1 only) Predicate returning true or false depending on whether this Rule is an ParameterRule.
abstract 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).
boolean	isSetUnits() Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
boolean	isSetUnitsInstance() Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
boolean	isSetVariable() Returns true if the variableID of this Assignment is not null.
boolean	isSetVariableInstance() Returns true if the Variable instance which has the variableID of this Assignment as id is not null.
boolean	isSpeciesConcentration() (SBML Level 1 only) Predicate returning true or false depending on whether this Rule is an SpeciesConcentrationRule.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setUnits(java.lang.String unitsID) Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
void	setUnits(Unit.Kind unitKind) Deprecated.
void	setUnits(Unit unit) Deprecated.
void	setUnits(UnitDefinition units) Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
void	setVariable(java.lang.String variable) Sets the variableID of this Assignment to the given value.
void	setVariable(Variable variable) Sets the variableID of this Assignment to the id of the Variable 'variable'.Listeners are notified about this change.
void	unsetUnits() Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this ExplicitRule represents the SBML element ParameterRule.
void	unsetVariable() Removes the reference from this InitialAssignment to its Variable if there was any, i.e., the Variable is set to null.
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.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, unsetFormula, unsetMath

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, 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, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setLevelAndVersion, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageNamespaceAndVersion, 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, isLeaf, isReadingInProgress, 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, 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, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, 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 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

unitsID

@Deprecated
protected java.lang.String unitsID

Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.

Represents the 'units' XML attribute of a ParameterRule.

variableID

java.lang.String variableID

Represents the id of a Variable. Matches the variable XML attribute of an assignmentRule or rateRule element.

Constructor Detail

ExplicitRule

public ExplicitRule()

Creates a new ExplicitRule.

ExplicitRule

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

Creates a new ExplicitRule

Parameters:

math -

level -

version -

ExplicitRule

public ExplicitRule(ASTNode math,
                    Variable variable)

Creates a new ExplicitRule with the given ASTNode element for the assignment to the given Variable or the derivative of the Variable.

Parameters:

math - An assignment

variable - Either the variable itself or its derivative is to be modified with the given.

ExplicitRule

public ExplicitRule(ExplicitRule rule)

Creates a new ExplicitRule

Parameters:

rule -

ExplicitRule

public ExplicitRule(int level,
                    int version)

Creates a new ExplicitRule

Parameters:

level -

version -

ExplicitRule

public ExplicitRule(Parameter parameter)

Creates a new ExplicitRule

Parameters:

parameter -

ExplicitRule

public ExplicitRule(Parameter parameter,
                    ASTNode math)

Creates a new ExplicitRule

Parameters:

parameter -

math -

ExplicitRule

public ExplicitRule(Variable variable)

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

Parameters:

variable -

ExplicitRule

public ExplicitRule(Variable variable,
                    ASTNode math)

Creates a new ExplicitRule

Parameters:

variable -

math -

Method Detail

clone

public abstract ExplicitRule 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 Rule

Returns:

a copy of this object

equals

public boolean equals(java.lang.Object object)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

Parameters:

object - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.

getUnits

@Deprecated
public java.lang.String getUnits()

Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.

Returns the unitsID of this object.

Specified by:

getUnits in interface SBaseWithUnit

Returns:

the unitsID of this object.

getUnitsInstance

@Deprecated
public UnitDefinition getUnitsInstance()

Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.

Specified by:

getUnitsInstance in interface SBaseWithUnit

Returns:

the UnitDefinition instance which matches the unitsID of this object.

getVariable

public java.lang.String getVariable()

Description copied from interface: Assignment

Returns the variableID of this Assignment. Returns an empty String if it is not set.

Specified by:

getVariable in interface Assignment

Returns:

the variableID of this Assignment. Returns an empty String if it is not set.

getVariableInstance

public Variable getVariableInstance()

Description copied from interface: Assignment

Returns the Variable instance which has the variableID of this Assignment as id. Return null if it doesn't exist.

Specified by:

getVariableInstance in interface Assignment

Returns:

the Variable instance which has the variableID of this Assignment as id. Return null if it doesn't exist.

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

initDefaults

public void initDefaults()

isCompartmentVolume

public boolean isCompartmentVolume()

Description copied from class: Rule

(SBML Level 1 only) Predicate returning true or false depending on whether this Rule is an CompartmentVolumeRule.

Specified by:

isCompartmentVolume in class Rule

Returns:

true if this Rule is a CompartmentVolumeRule, false otherwise.

isParameter

public boolean isParameter()

Description copied from class: Rule

(SBML Level 1 only) Predicate returning true or false depending on whether this Rule is an ParameterRule.

Specified by:

isParameter in class Rule

Returns:

true if this Rule is a ParameterRule, false otherwise.

isScalar

public abstract 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).

Returns:

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

isSetUnits

@Deprecated
public boolean isSetUnits()

Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.

Specified by:

isSetUnits in interface SBaseWithUnit

Returns:

true if the unitsID of this object is not null.

isSetUnitsInstance

@Deprecated
public boolean isSetUnitsInstance()

Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.

Description copied from interface: SBaseWithUnit

Checks whether the element referenced by the unitsID attribute of this SBaseWithUnit is either an existing base Unit, i.e., a simple Unit that can directly be addressed via its Unit.Kind element, or the identifier of an existing UnitDefinition in the Model to which this SBaseWithUnit belongs.

Specified by:

isSetUnitsInstance in interface SBaseWithUnit

Returns:

true if the UnitsID of this object matches a no null UniDefinition of the model instance.

isSetVariable

public boolean isSetVariable()

Description copied from interface: Assignment

Returns true if the variableID of this Assignment is not null.

Specified by:

isSetVariable in interface Assignment

Returns:

true if the variableID of this Assignment is not null.

isSetVariableInstance

public boolean isSetVariableInstance()

Description copied from interface: Assignment

Returns true if the Variable instance which has the variableID of this Assignment as id is not null.

Specified by:

isSetVariableInstance in interface Assignment

Returns:

true if the Variable instance which has the variableID of this Assignment as id is not null.

isSpeciesConcentration

public boolean isSpeciesConcentration()

Description copied from class: Rule

(SBML Level 1 only) Predicate returning true or false depending on whether this Rule is an SpeciesConcentrationRule.

Specified by:

isSpeciesConcentration in class Rule

Returns:

true if this Rule is a SpeciesConcentrationRule, false otherwise.

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 AbstractMathContainer

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.

setUnits

@Deprecated
public void setUnits(Unit.Kind unitKind)

Deprecated.

Description copied from interface: SBaseWithUnit

Sets the unit of this SBaseWithUnit. A new unit will be created base on this kind.

Specified by:

setUnits in interface SBaseWithUnit

setUnits

@Deprecated
public void setUnits(java.lang.String unitsID)

Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.

Sets the unitsID to 'unitsID'.

Specified by:

setUnits in interface SBaseWithUnit

Parameters:

unitsID - A valid identifier of a UnitDefinition in the Model or the name of one of the Unit.Kind base types.

Throws:

PropertyNotAvailableException - if Level is not 1.

setUnits

@Deprecated
public void setUnits(Unit unit)

Deprecated.

Description copied from interface: SBaseWithUnit

Sets the Unit of this SBaseWithUnit.

Specified by:

setUnits in interface SBaseWithUnit

setUnits

@Deprecated
public void setUnits(UnitDefinition units)

Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.

Sets the unitsID of this object with the id of 'units'.

Specified by:

setUnits in interface SBaseWithUnit

Parameters:

units - the unit of this rule.

setVariable

public void setVariable(java.lang.String variable)

Description copied from interface: Assignment

Sets the variableID of this Assignment to the given value. Listeners are notified about this change.

Specified by:

setVariable in interface Assignment

Parameters:

variable - the variable to set

setVariable

public void setVariable(Variable variable)

Description copied from interface: Assignment

Sets the variableID of this Assignment to the id of the Variable 'variable'.Listeners are notified about this change.

Specified by:

setVariable in interface Assignment

Parameters:

variable - the variable to set

unsetUnits

@Deprecated
public void unsetUnits()

Deprecated. This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this ExplicitRule represents the SBML element ParameterRule.

Unsets the unitsID of this ExplicitRule.

Specified by:

unsetUnits in interface SBaseWithUnit

unsetVariable

public void unsetVariable()

Description copied from interface: Assignment

Removes the reference from this InitialAssignment to its Variable if there was any, i.e., the Variable is set to null. Listeners are notified about this change.

Specified by:

unsetVariable in interface Assignment

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 AbstractMathContainer

Returns:

a Map containing the XML attributes of this object.