org.sbml.jsbml

Class KineticLaw

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractMathContainer

org.sbml.jsbml.KineticLaw

All Implemented Interfaces:

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

public class KineticLaw
extends AbstractMathContainer
implements SBaseWithUnit, IdManager, UniqueSId

Represents the kineticLaw XML element of a SBML file.

Since:

0.8

Author:

Andreas Dräger, Marine Dumousseau

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private static java.lang.String	ILLEGAL_UNIT_KIND_EXCEPTION_MSG Exception to be displayed in case that an illegal variant of unit is to be set for this SBaseWithUnit.
private ListOf<LocalParameter>	listOfLocalParameters Represents the listOfLocalParameters or listOfParameters sub-element of a kineticLaw element.
private static org.apache.log4j.Logger	logger A logger for this class.
private java.util.Map<java.lang.String,LocalParameter>	mapOfLocalParameters For internal computation: a mapping between their identifiers and the LocalParameters in KineticLaws themselves:
private static long	serialVersionUID Generated serial version identifier.
private java.lang.String	substanceUnitsID Deprecated.
private java.lang.String	timeUnitsID Deprecated.
private java.lang.String	unitsID Deprecated.

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
KineticLaw() Creates a KineticLaw instance.
KineticLaw(int level, int version) Creates a KineticLaw instance from a level and version.
KineticLaw(KineticLaw kineticLaw) Creates a KineticLaw instance from a given KineticLaw.
KineticLaw(Reaction parentReaction) Creates a KineticLaw instance from a given Reaction.

Method Summary

Modifier and Type	Method and Description
boolean	accept(SBase sbase) Returns true if this IdManager can register or unregister the given SBase.
boolean	addLocalParameter(LocalParameter parameter) Adds a copy of the given Parameter object to the list of local parameters in this KineticLaw.
boolean	addParameter(LocalParameter parameter) Deprecated. use addLocalParameter(LocalParameter).
void	addParameter(Parameter p) Deprecated. A KineticLaw can only contain instances of LocalParameters. Please use addLocalParameter(LocalParameter) and create an instance of LocalParameter for your purposes.
KineticLaw	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
LocalParameter	createLocalParameter()
LocalParameter	createLocalParameter(java.lang.String id)
boolean	equals(java.lang.Object object) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
ListOf<LocalParameter>	getListOfLocalParameters()
ListOf<LocalParameter>	getListOfParameters() Deprecated. use getListOfLocalParameters()
LocalParameter	getLocalParameter(int i)
LocalParameter	getLocalParameter(java.lang.String id)
int	getLocalParameterCount()
int	getNumLocalParameters() Deprecated. use getLocalParameterCount()
int	getNumParameters() Deprecated. use getLocalParameterCount()
LocalParameter	getParameter(int i) Deprecated. use getLocalParameter(int)
LocalParameter	getParameter(java.lang.String id) Deprecated. use getLocalParameter(String)
Reaction	getParent() This is equivalent to calling AbstractSBase.getParentSBMLObject(), but this method is needed for TreeNode.
Reaction	getParentSBMLObject() This method is convenient when holding an object nested inside other objects in an SBML model.
java.lang.String	getSubstanceUnits() Deprecated.
UnitDefinition	getSubstanceUnitsInstance() Deprecated.
java.lang.String	getTimeUnits() Deprecated.
UnitDefinition	getTimeUnitsInstance() Deprecated.
java.lang.String	getUnits() Deprecated.
UnitDefinition	getUnitsInstance() Deprecated.
int	hashCode() Returns a hash code value for this SBase instance.
void	initDefaults()
boolean	isListOfLocalParametersEmpty() Returns true, if the list of local parameters is not null.
boolean	isSetListOfLocalParameters() Returns true, if the list of local parameters is set and not empty..
boolean	isSetListOfParameters() Deprecated. use isSetListOfLocalParameters()
boolean	isSetSubstanceUnits() Deprecated.
boolean	isSetSubstanceUnitsInstance() Deprecated.
boolean	isSetTimeUnits() Deprecated.
boolean	isSetTimeUnitsInstance() Deprecated.
boolean	isSetUnits() Deprecated.
boolean	isSetUnitsInstance() Deprecated.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
boolean	register(SBase sbase) Registers the given SBase element and all of it's children in this IdManager.
private boolean	register(SBase sbase, boolean unregister)
(package private) boolean	registerLocalParameter(LocalParameter parameter, boolean delete)
LocalParameter	removeLocalParameter(int i) Removes the ith LocalParameter from this object.
boolean	removeLocalParameter(LocalParameter p) Removes the LocalParameter 'p' from the listOfLocalParameters of this KineticLaw according to its 'id'.
boolean	removeLocalParameter(java.lang.String id) Removes a LocalParameter from this object based on its 'id'.
void	removeParameter(int i) Deprecated. use removeLocalParameter(int)
boolean	removeParameter(Parameter p) Deprecated. use removeLocalParameter(LocalParameter)
boolean	removeParameter(java.lang.String id) Deprecated. use removeLocalParameter(String)
void	setListOfLocalParameters(ListOf<LocalParameter> listOfLocalParameters) Sets the listOfParameters of this KineticLaw to 'list'.
void	setSubstanceUnits(java.lang.String substanceUnits) Deprecated. Only defined for SBML Level 1 and Level 2 Version 1 and 2.
void	setSubstanceUnits(Unit substanceUnit) Deprecated.
void	setTimeUnits(java.lang.String timeUnits) Deprecated. Only defined for Level 1 and Level 2 Version 1.
void	setTimeUnits(Unit timeUnit) Deprecated.
void	setTimeUnits(UnitDefinition timeUnits) Deprecated. Only defined for Level 1 and Level 2 Version 1.
void	setUnits(java.lang.String units) Deprecated.
void	setUnits(Unit.Kind unitKind) Deprecated.
void	setUnits(Unit unit) Deprecated.
void	setUnits(UnitDefinition units) Deprecated.
boolean	unregister(SBase sbase) Unregisters the given SBase element and all of it's children in this IdManager.
boolean	unsetListOfLocalParameters() Removes the listOfLocalParameters from this KineticLaw and notifies all registered instances of TreeNodeChangeListener.
void	unsetListOfParameters() Deprecated. use unsetListOfLocalParameters()
void	unsetSubstanceUnits() Deprecated.
void	unsetTimeUnits() Deprecated.
void	unsetUnits() Deprecated.
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.AbstractMathContainer

containsUndeclaredUnits, getAllowsChildren, 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, 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.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, 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, getIndex, isLeaf

Field Detail

ILLEGAL_UNIT_KIND_EXCEPTION_MSG

private static final java.lang.String ILLEGAL_UNIT_KIND_EXCEPTION_MSG

Exception to be displayed in case that an illegal variant of unit is to be set for this SBaseWithUnit.

See Also:

Constant Field Values

logger

private static final transient org.apache.log4j.Logger logger

A logger for this class.

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

listOfLocalParameters

private ListOf<LocalParameter> listOfLocalParameters

Represents the listOfLocalParameters or listOfParameters sub-element of a kineticLaw element.

mapOfLocalParameters

private java.util.Map<java.lang.String,LocalParameter> mapOfLocalParameters

For internal computation: a mapping between their identifiers and the LocalParameters in KineticLaws themselves:

substanceUnitsID

@Deprecated
private java.lang.String substanceUnitsID

Deprecated.

Represents the 'substanceUnits' XML attribute of this KineticLaw.

timeUnitsID

@Deprecated
private java.lang.String timeUnitsID

Deprecated.

Represents the 'timeUnits' XML attribute of this KineticLaw.

unitsID

@Deprecated
private java.lang.String unitsID

Deprecated.

In case that a variant of substance per time is set, this will memorize the identifier of the corresponding element in the Model.

Constructor Detail

KineticLaw

public KineticLaw()

Creates a KineticLaw instance. By default, this listOfParameters, the timeUnitsID and substanceUnitsID are null.

KineticLaw

public KineticLaw(int level,
                  int version)

Creates a KineticLaw instance from a level and version. By default, this listOfParameters, the timeUnitsID and substanceUnitsID are null.

Parameters:

level -

version -

KineticLaw

public KineticLaw(KineticLaw kineticLaw)

Creates a KineticLaw instance from a given KineticLaw.

Parameters:

kineticLaw -

KineticLaw

public KineticLaw(Reaction parentReaction)

Creates a KineticLaw instance from a given Reaction.

Parameters:

parentReaction -

Method Detail

accept

public boolean accept(SBase sbase)

Description copied from interface: IdManager

Returns true if this IdManager can register or unregister the given SBase.

Specified by:

accept in interface IdManager

Returns:

true if this IdManager can register or unregister the given SBase.

addLocalParameter

public boolean addLocalParameter(LocalParameter parameter)

Adds a copy of the given Parameter object to the list of local parameters in this KineticLaw.

Parameters:

parameter -

Returns:

true if the listOfLocalParameters was changed as a result of this call.

addParameter

@Deprecated
public boolean addParameter(LocalParameter parameter)

Deprecated. use addLocalParameter(LocalParameter).

Adds a copy of the given Parameter object to the list of local parameters in this KineticLaw.

Parameters:

parameter -

Returns:

true if the listOfLocalParameters was changed as a result of this call.

addParameter

@Deprecated
public void addParameter(Parameter p)

Deprecated. A KineticLaw can only contain instances of LocalParameters. Please use addLocalParameter(LocalParameter) and create an instance of LocalParameter for your purposes.

Creates a new LocalParameter with identical properties as the given Parameter and adds this new LocalParameter to this KineticLaw's listOfLocalParameters.

Parameters:

p -

clone

public KineticLaw 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 AbstractMathContainer

Returns:

a copy of this object

createLocalParameter

public LocalParameter createLocalParameter()

Returns:

createLocalParameter

public LocalParameter createLocalParameter(java.lang.String id)

Parameters:

id -

Returns:

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.

getChildAt

public javax.swing.tree.TreeNode getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractMathContainer

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class AbstractMathContainer

getListOfLocalParameters

public ListOf<LocalParameter> getListOfLocalParameters()

Returns:

the listOfLocalParameters of this KineticLaw. Returns null if it is not set.

getListOfParameters

@Deprecated
public ListOf<LocalParameter> getListOfParameters()

Deprecated. use getListOfLocalParameters()

Returns:

the listOfLocalParameters of this KineticLaw. Returns null if it is not set.

getLocalParameter

public LocalParameter getLocalParameter(int i)

Parameters:

i -

Returns:

the ith LocalParameter object in the listOfLocalParameters in this KineticLaw instance.

getLocalParameter

public LocalParameter getLocalParameter(java.lang.String id)

Parameters:

id -

Returns:

a LocalParameter based on its identifier.

getLocalParameterCount

public int getLocalParameterCount()

Returns:

the number of LocalParameter instances in this KineticLaw instance.

getNumLocalParameters

@Deprecated
public int getNumLocalParameters()

Deprecated. use getLocalParameterCount()

Returns:

the number of LocalParameter instances in this KineticLaw instance.

getNumParameters

@Deprecated
public int getNumParameters()

Deprecated. use getLocalParameterCount()

Returns:

the number of LocalParameter instances in this KineticLaw instance.

getParameter

@Deprecated
public LocalParameter getParameter(int i)

Deprecated. use getLocalParameter(int)

Parameters:

i -

Returns:

the ith LocalParameter object in the listOfLocalParameters in this KineticLaw instance.

getParameter

@Deprecated
public LocalParameter getParameter(java.lang.String id)

Deprecated. use getLocalParameter(String)

Parameters:

id -

Returns:

a LocalParameter based on its identifier.

getParent

public Reaction getParent()

Description copied from class: AbstractSBase

This is equivalent to calling AbstractSBase.getParentSBMLObject(), but this method is needed for TreeNode.

Specified by:

getParent in interface javax.swing.tree.TreeNode

Overrides:

getParent in class AbstractSBase

Returns:

the parent element of this element.

See Also:

AbstractSBase.getParentSBMLObject()

getParentSBMLObject

public Reaction getParentSBMLObject()

This method is convenient when holding an object nested inside other objects in an SBML model. It allows direct access to the <model> element containing it.

Specified by:

getParentSBMLObject in interface SBase

Overrides:

getParentSBMLObject in class AbstractSBase

Returns:

the parent SBML object.

See Also:

TreeNode.getParent()

getSubstanceUnits

@Deprecated
public java.lang.String getSubstanceUnits()

Deprecated.

Returns:

the substanceUnitsID of this KineticLaw. Return the empty String if it is not set.

getSubstanceUnitsInstance

@Deprecated
public UnitDefinition getSubstanceUnitsInstance()

Deprecated.

Returns:

the UnitDefinition instance which has the substanceUnistID of this KineticLaw as id. Return null if it doesn't exist.

getTimeUnits

@Deprecated
public java.lang.String getTimeUnits()

Deprecated.

Returns:

the timeUnitsID of this KineticLaw. Return the empty String if it is not set.

getTimeUnitsInstance

@Deprecated
public UnitDefinition getTimeUnitsInstance()

Deprecated.

Returns:

the UnitDefinition instance which has the timeUnistID of this KineticLaw as id. Return null if it doesn't exist.

getUnits

@Deprecated
public java.lang.String getUnits()

Deprecated.

Specified by:

getUnits in interface SBaseWithUnit

Returns:

the unitsID of this SBaseWithUnit. The empty String if it is not set.

getUnitsInstance

@Deprecated
public UnitDefinition getUnitsInstance()

Deprecated.

Specified by:

getUnitsInstance in interface SBaseWithUnit

Returns:

The UnitDefinition instance which has the unitsID of this SBaseWithUnit as id. Null if it doesn't exist. In case that the unit of this SBaseWithUnit represents a base Unit, a new UnitDefinition will be created and returned by this method. This new UnitDefinition will only contain the one unit represented by the unit identifier in this SBaseWithUnit. Note that the corresponding model will not contain this UnitDefinition. The identifier of this new UnitDefinition will be set to the same value as the name of the base Unit.

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()

isListOfLocalParametersEmpty

public boolean isListOfLocalParametersEmpty()

Returns true, if the list of local parameters is not null.

Returns:

true, if the list of local parameters is not null.

isSetListOfLocalParameters

public boolean isSetListOfLocalParameters()

Returns true, if the list of local parameters is set and not empty..

isSetListOfParameters

@Deprecated
public boolean isSetListOfParameters()

Deprecated. use isSetListOfLocalParameters()

Returns:

true if the listOfParameters of this KineticLaw is not null and not empty.

isSetSubstanceUnits

@Deprecated
public boolean isSetSubstanceUnits()

Deprecated.

Returns:

true if the substanceUnitsID of this KineticLaw is not null.

isSetSubstanceUnitsInstance

@Deprecated
public boolean isSetSubstanceUnitsInstance()

Deprecated.

Returns:

true if the UnistDefinition instance which has the substanceUnitsID of this KineticLaw as id is not null.

isSetTimeUnits

@Deprecated
public boolean isSetTimeUnits()

Deprecated.

Returns:

true if the timeUnitsID of this KineticLaw is not null.

isSetTimeUnitsInstance

@Deprecated
public boolean isSetTimeUnitsInstance()

Deprecated.

Returns:

true if the UnistDefinition instance which has the timeUnitsID of this KineticLaw as id is not null.

isSetUnits

@Deprecated
public boolean isSetUnits()

Deprecated.

Specified by:

isSetUnits in interface SBaseWithUnit

Returns:

true if the unitsID of this element is not null.

isSetUnitsInstance

@Deprecated
public boolean isSetUnitsInstance()

Deprecated.

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 either a UnitDefinition, which has the unitsID of this SBaseWithUnit, can be found in the Model to which this SBaseWithUnit belongs, or if this element's unitsID as a corresponding base Unit for the given Level/Version combination.

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.

register

public boolean register(SBase sbase)

Description copied from interface: IdManager

Registers the given SBase element and all of it's children in this IdManager.

Specified by:

register in interface IdManager

Returns:

true if this operation was successfully performed, false otherwise.

register

private boolean register(SBase sbase,
                         boolean unregister)

Parameters:

sbase -

unregister -

Returns:

registerLocalParameter

boolean registerLocalParameter(LocalParameter parameter,
                               boolean delete)

Parameters:

parameter -

delete -

Returns:

removeLocalParameter

public LocalParameter removeLocalParameter(int i)

Removes the ith LocalParameter from this object.

Parameters:

i -

Returns:

the LocalParameter that has been removed or null.

removeLocalParameter

public boolean removeLocalParameter(LocalParameter p)

Removes the LocalParameter 'p' from the listOfLocalParameters of this KineticLaw according to its 'id'.

Parameters:

p -

Returns:

true if the operation was performed successfully.

removeLocalParameter

public boolean removeLocalParameter(java.lang.String id)

Removes a LocalParameter from this object based on its 'id'.

Parameters:

id -

Returns:

true if the operation was performed successfully.

removeParameter

@Deprecated
public void removeParameter(int i)

Deprecated. use removeLocalParameter(int)

Removes the ith LocalParameter from this object.

Parameters:

i -

removeParameter

@Deprecated
public boolean removeParameter(Parameter p)

Deprecated. use removeLocalParameter(LocalParameter)

Removes the Parameter 'p' from the listOfLocalParameters of this KineticLaw.

Parameters:

p -

Returns:

true if the operation was performed successfully.

removeParameter

@Deprecated
public boolean removeParameter(java.lang.String id)

Deprecated. use removeLocalParameter(String)

Removes a LocalParameter from this object based on its 'id'.

Parameters:

id -

Returns:

true if the operation was performed successfully.

setListOfLocalParameters

public void setListOfLocalParameters(ListOf<LocalParameter> listOfLocalParameters)

Sets the listOfParameters of this KineticLaw to 'list'. It automatically sets this as parentSBML object of the listOfParameters as well as the Parameter instances in the list.

Parameters:

listOfLocalParameters -

setSubstanceUnits

@Deprecated
public void setSubstanceUnits(java.lang.String substanceUnits)

Deprecated. Only defined for SBML Level 1 and Level 2 Version 1 and 2.

Sets the substanceUnitsID of this KineticLaw.

Parameters:

substanceUnits -

Throws:

PropertyNotAvailableException - for inappropriate Level/Version combinations.

setSubstanceUnits

@Deprecated
public void setSubstanceUnits(Unit substanceUnit)

Deprecated.

Parameters:

substanceUnit -

setTimeUnits

@Deprecated
public void setTimeUnits(java.lang.String timeUnits)

Deprecated. Only defined for Level 1 and Level 2 Version 1.

Sets the timeUnitsID of this KineticLaw.

Parameters:

timeUnits -

Throws:

PropertyNotAvailableException - for inappropriate Level/Version combinations.

setTimeUnits

@Deprecated
public void setTimeUnits(Unit timeUnit)

Deprecated.

Parameters:

timeUnit -

setTimeUnits

@Deprecated
public void setTimeUnits(UnitDefinition timeUnits)

Deprecated. Only defined for Level 1 and Level 2 Version 1.

Sets the timeUnitsID of this KineticLaw.

Parameters:

timeUnits -

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 units)

Deprecated.

Description copied from interface: SBaseWithUnit

Sets the unitsID of this SBaseWithUnit. Only valid unit kind names or identifiers of already existing UnitDefinitions are allowed arguments of this function.

Specified by:

setUnits in interface SBaseWithUnit

Parameters:

units - the identifier of an already existing UnitDefinition or an Unit.Kind identifier for the current level/version combination of this unit. Passing a null value to this method is equivalent to calling SBaseWithUnit.unsetUnits().

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.

Description copied from interface: SBaseWithUnit

Set the unit attribute of this SBaseWithUnit to the given unit definition.

Specified by:

setUnits in interface SBaseWithUnit

unregister

public boolean unregister(SBase sbase)

Description copied from interface: IdManager

Unregisters the given SBase element and all of it's children in this IdManager.

Specified by:

unregister in interface IdManager

Returns:

true if this operation was successfully performed, false otherwise.

unsetListOfLocalParameters

public boolean unsetListOfLocalParameters()

Removes the listOfLocalParameters from this KineticLaw and notifies all registered instances of TreeNodeChangeListener.

Returns:

true if calling this method lead to a change in this data structure.

unsetListOfParameters

@Deprecated
public void unsetListOfParameters()

Deprecated. use unsetListOfLocalParameters()

unsetSubstanceUnits

@Deprecated
public void unsetSubstanceUnits()

Deprecated.

Unsets the sunbstanceUnistID of this KineticLaw.

unsetTimeUnits

@Deprecated
public void unsetTimeUnits()

Deprecated.

Unsets the timeUnitsID of this KineticLaw.

unsetUnits

@Deprecated
public void unsetUnits()

Deprecated.

Description copied from interface: SBaseWithUnit

Sets the unitsID of this SBaseWithUnit to null.

Specified by:

unsetUnits in interface SBaseWithUnit

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.