org.sbml.jsbml

Class LocalParameter

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.AbstractNamedSBaseWithUnit

org.sbml.jsbml.QuantityWithUnit

org.sbml.jsbml.LocalParameter

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, CallableSBase, NamedSBase, NamedSBaseWithDerivedUnit, Quantity, SBase, SBaseWithDerivedUnit, SBaseWithUnit, TreeNodeWithChangeSupport

public class LocalParameter
extends QuantityWithUnit

A local parameter can only be used to specify a constant within a KineticLaw.

Since:

0.8

Version:

$Rev: 1690 $

Author:

Andreas Dräger, Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	isExplicitlySetConstant This field memorizes whether this LocalParameter has been explicitly set to be constant.
private static long	serialVersionUID Generated serial version identifier.

Fields inherited from class org.sbml.jsbml.QuantityWithUnit

value

Fields inherited from class org.sbml.jsbml.AbstractNamedSBaseWithUnit

unitsID

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

Constructor Summary

Constructors

Constructor and Description
LocalParameter() Creates a new instance of LocalParameter.
LocalParameter(int level, int version)
LocalParameter(LocalParameter lp)
LocalParameter(Parameter parameter) Creates a new local parameter that will have the same properties than the given global parameter.
LocalParameter(java.lang.String id) Creates a new instance of LocalParameter with the given identifier.
LocalParameter(java.lang.String id, int level, int version)
LocalParameter(java.lang.String id, java.lang.String name, int level, int version)

Method Summary

Methods

Modifier and Type	Method and Description
LocalParameter	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	getElementName() Returns the XML element name of this object.
ListOf<LocalParameter>	getParent() This is equivalent to calling AbstractSBase.getParentSBMLObject(), but this method is needed for TreeNode.
ListOf<LocalParameter>	getParentSBMLObject() Returns the parent of this SBase.
java.lang.String	getPredefinedUnitID() Returns the predefined unit identifier for this data type with the current level/version combination.
int	hashCode() Returns a hash code value for this SBase instance.
boolean	isExplicitlySetConstant() In SBML prior to Level 3 it was possible to explicitly state that a local parameter represents a constant Quantity.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setExplicitlyConstant(boolean isExplicitlySetConstant) Deprecated. Since SBML Level 3 it is no longer possible to explicitly set a LocalParameter to constant = true because LocalParameter instances always represent constant a Quantity.
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.QuantityWithUnit

getValue, isIdMandatory, isSetValue, setValue, unsetValue

Methods inherited from class org.sbml.jsbml.AbstractNamedSBaseWithUnit

containsUndeclaredUnits, getDerivedUnitDefinition, getDerivedUnits, getUnits, getUnitsInstance, isPredefinedUnitsID, isSetUnits, isSetUnitsInstance, setUnits, setUnits, setUnits, setUnits, unsetUnits

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

checkIdentifier, getId, getName, 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, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, 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.NamedSBase

getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

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, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, 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, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

isExplicitlySetConstant

private boolean isExplicitlySetConstant

This field memorizes whether this LocalParameter has been explicitly set to be constant. All instances of LocalParameter are constant by definition, however, in earlier versions of SBML (before Level 3) it was possible to explicitly state that a LocalParameter is constant. Therefore, a special field has become necessary to reflect this property.

Constructor Detail

LocalParameter

public LocalParameter()

Creates a new instance of LocalParameter.

LocalParameter

public LocalParameter(int level,
              int version)

Parameters:

level -

version -

LocalParameter

public LocalParameter(LocalParameter lp)

Parameters:

lp -

LocalParameter

public LocalParameter(Parameter parameter)

Creates a new local parameter that will have the same properties than the given global parameter. However, the value of the constant attribute will be ignored because a local parameter can only be a constant quantity.

Parameters:

parameter -

LocalParameter

public LocalParameter(java.lang.String id)

Creates a new instance of LocalParameter with the given identifier.

Parameters:

id -

LocalParameter

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

Parameters:

id -

level -

version -

LocalParameter

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

Parameters:

id -

name -

level -

version -

Method Detail

clone

public LocalParameter 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 QuantityWithUnit

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 QuantityWithUnit

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.

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.

getParent

public ListOf<LocalParameter> 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 ListOf<LocalParameter> getParentSBMLObject()

Description copied from interface: SBase

Returns the parent of this SBase.

Specified by:

getParentSBMLObject in interface SBase

Overrides:

getParentSBMLObject in class AbstractSBase

Returns:

the parent SBML object.

See Also:

TreeNode.getParent()

getPredefinedUnitID

public java.lang.String getPredefinedUnitID()

Description copied from class: AbstractNamedSBaseWithUnit

Returns the predefined unit identifier for this data type with the current level/version combination.

Specified by:

getPredefinedUnitID in class AbstractNamedSBaseWithUnit

Returns:

an identifier of a unit in the containing Model. This can be one of the predefined unit identifiers if there are any.

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 QuantityWithUnit

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

isExplicitlySetConstant

public boolean isExplicitlySetConstant()

In SBML prior to Level 3 it was possible to explicitly state that a local parameter represents a constant Quantity. However, per definition, each local parameter has always been constant no matter if its XML representation contains the constant attribute or not. Hence, this attribute could set to true only. This method checks if for this LocalParameter an explicit constant flag has been set.

Returns:

the isExplicitlySetConstant true if this LocalParameter contains an explicit constant flag, 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 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.

setExplicitlyConstant

@Deprecated
public void setExplicitlyConstant(boolean isExplicitlySetConstant)

Deprecated. Since SBML Level 3 it is no longer possible to explicitly set a LocalParameter to constant = true because LocalParameter instances always represent constant a Quantity.

This method allows users to explicitly manipulate the constant attribute of this LocalParameter. This attribute can set to true only. Therefore, this method does just decide whether or not the constant attribute should occur in generated SBML code when serializing this LocalParameter . Since this object always represents a constant Quantity this method does only decide whether or not the resulting SBML code should contain the attribute/value pair constant = true, it does not decide on whether or not this object should be constant.

Parameters:

isExplicitlySetConstant - the isExplicitlySetConstant to set

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.