org.sbml.jsbml

Class InitialAssignment

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractMathContainer

org.sbml.jsbml.InitialAssignment

All Implemented Interfaces:

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

public class InitialAssignment
extends AbstractMathContainer
implements Assignment

Represents the initialAssignment XML element of a SBML file.

Since:

0.8

Author:

Andreas Dräger, Marine Dumousseau

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

JSBML_WRONG_SBO_TERM

Constructor Summary

Constructors

Constructor and Description
InitialAssignment() Creates an InitialAssignment instance.
InitialAssignment(InitialAssignment sb) Creates an InitialAssignment instance from a given InitialAssignment.
InitialAssignment(int level, int version) Creates an InitialAssignment from level and version.
InitialAssignment(Variable variable) Creates an InitialAssignment instance from a Variable.
InitialAssignment(Variable variable, ASTNode math, int level, int version) Creates an InitialAssignment from a Variable, ASTNode, level and version.

Method Summary

Modifier and Type	Method and Description
void	checkAndSetVariable(java.lang.String variable) Sets the variableID of this InitialAssignment to 'variable'.
InitialAssignment	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.
ListOf<InitialAssignment>	getParent() This is equivalent to calling AbstractSBase.getParentSBMLObject(), but this method is needed for TreeNode.
java.lang.String	getSymbol() Deprecated. use getVariable()
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.
boolean	isSetSymbol()
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	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setSymbol(java.lang.String symbol) Deprecated. use setVariable(String).
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	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.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, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, 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, isValidLevelAndVersionCombination, isValidMetaId, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, 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, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

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, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, 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, isLeaf

Constructor Detail

InitialAssignment

public InitialAssignment()

Creates an InitialAssignment instance. By default, variableID is null.

InitialAssignment

public InitialAssignment(InitialAssignment sb)

Creates an InitialAssignment instance from a given InitialAssignment.

Parameters:

sb -

InitialAssignment

public InitialAssignment(int level,
                         int version)

Creates an InitialAssignment from level and version.

Parameters:

level -

version -

InitialAssignment

public InitialAssignment(Variable variable)

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

Parameters:

variable -

InitialAssignment

public InitialAssignment(Variable variable,
                         ASTNode math,
                         int level,
                         int version)

Creates an InitialAssignment from a Variable, ASTNode, level and version.

Parameters:

variable -

math -

level -

version -

Method Detail

checkAndSetVariable

public void checkAndSetVariable(java.lang.String variable)

Sets the variableID of this InitialAssignment to 'variable'. If this variableID doesn't match any Variable id in Model ( Compartment, Species, SpeciesReference, or Parameter), an IllegalArgumentException is thrown.

Parameters:

variable - the symbol to set

clone

public InitialAssignment 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

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.

getParent

public ListOf<InitialAssignment> 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()

getSymbol

@Deprecated
public java.lang.String getSymbol()

Deprecated. use getVariable()

This method is for compatibility with libSBML only.

Returns:

the variableID of this InitialAssignment. Return an empty String if it is not set.

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()

isSetSymbol

public boolean isSetSymbol()

Returns:

true if the variableID of this InitialAssignment is not null.

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.

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.

setSymbol

@Deprecated
public void setSymbol(java.lang.String symbol)

Deprecated. use setVariable(String).

This method is provided for compatibility with libSBML and also to reflect what is written in the SBML specifications until L3V1, but for consistency, JSBML uses the term Variable to refer to elements that satisfy the properties of this interface.

Parameters:

symbol -

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

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.