org.sbml.jsbml

Class FunctionDefinition

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractMathContainer

org.sbml.jsbml.FunctionDefinition

All Implemented Interfaces:

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

public class FunctionDefinition
extends AbstractMathContainer
implements CallableSBase, UniqueNamedSBase

Represents the functionDefinition XML element of a SBML file. Since FunctionDefinitions were introduced to SBML in Level 2, this class must not be used for models in Level 1.

Since:

0.8

Version:

$Rev: 1690 $

Author:

Andreas Dräger, Marine Dumousseau

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	id Represents the "id" attribute of a functionDefinition element.
private static java.lang.String	ILLEGAL_ASTNODE_TYPE_MSG Error message to indicate that an incorrect ASTNode#Type has been passed to a method.
private java.lang.String	name Represents the "name" attribute of a functionDefinition element.
private static long	serialVersionUID Generated serial version identifier.

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
FunctionDefinition() Creates a FunctionDefinition instance.
FunctionDefinition(FunctionDefinition sb) Creates a FunctionDefinition instance from a given FunctionDefinition.
FunctionDefinition(int level, int version) Creates a FunctionDefinition instance from a level and version.
FunctionDefinition(java.lang.String id, ASTNode lambda, int level, int version) Creates a FunctionDefinition instance from an id, ASTNode, level and version.
FunctionDefinition(java.lang.String id, int level, int version) Creates a FunctionDefinition instance from an id, level and version.

Method Summary

Methods

Modifier and Type	Method and Description
(package private) boolean	checkIdentifier(java.lang.String sID) Checks if the sID is a valid identifier.
FunctionDefinition	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.
ASTNode	getArgument(int n) Get the nth argument to this function.
ASTNode	getArgument(java.lang.String name) Get the argument named name to this FunctionDefinition.
int	getArgumentCount() Get the number of arguments (bound variables) taken by this FunctionDefinition.
ASTNode	getBody() Get the mathematical expression that is the body of this FunctionDefinition object.
java.lang.String	getId()
java.lang.String	getName()
int	getNumArguments() Get the number of arguments (bound variables) taken by this FunctionDefinition.
ListOf<FunctionDefinition>	getParent() This is equivalent to calling AbstractSBase.getParentSBMLObject(), but this method is needed for TreeNode.
int	hashCode() Returns a hash code value for this SBase instance.
boolean	isIdMandatory() This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.
boolean	isSetId()
boolean	isSetName()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setId(java.lang.String id) sets the id value with 'id'
void	setMath(ASTNode math) Sets the math ASTNode of this MathContainer to the given value.
void	setName(java.lang.String name) sets the name value with 'name'.
java.lang.String	toString()
void	unsetId() sets the id value to null.
void	unsetName() sets the name value 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, 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.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, isLeaf

Field Detail

ILLEGAL_ASTNODE_TYPE_MSG

private static final java.lang.String ILLEGAL_ASTNODE_TYPE_MSG

Error message to indicate that an incorrect ASTNode#Type has been passed to a method.

See Also:

Constant Field Values

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

id

private java.lang.String id

Represents the "id" attribute of a functionDefinition element.

name

private java.lang.String name

Represents the "name" attribute of a functionDefinition element.

Constructor Detail

FunctionDefinition

public FunctionDefinition()

Creates a FunctionDefinition instance. By default, id and name are null.

FunctionDefinition

public FunctionDefinition(FunctionDefinition sb)

Creates a FunctionDefinition instance from a given FunctionDefinition.

Parameters:

sb -

FunctionDefinition

public FunctionDefinition(int level,
                  int version)

Creates a FunctionDefinition instance from a level and version. By default, name is null.

Parameters:

level -

version -

FunctionDefinition

public FunctionDefinition(java.lang.String id,
                  ASTNode lambda,
                  int level,
                  int version)

Creates a FunctionDefinition instance from an id, ASTNode, level and version. By default, name is null. If the ASTNode is not of type lambda, an IllegalArgumentException is thrown.

Parameters:

id -

lambda -

level -

version -

FunctionDefinition

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

Creates a FunctionDefinition instance from an id, level and version.

Parameters:

id -

level -

version -

Method Detail

checkIdentifier

boolean checkIdentifier(java.lang.String sID)

Checks if the sID is a valid identifier.

Parameters:

sID - the identifier to be checked. If null or an invalid identifier, an exception will be thrown.

Returns:

true only if the sID is a valid identifier. Otherwise this method throws an IllegalArgumentException. This is an intended behavior.

Throws:

java.lang.IllegalArgumentException - if the given id is not valid in this model.

clone

public FunctionDefinition 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.

getArgument

public ASTNode getArgument(int n)

Get the nth argument to this function. Callers should first find out the number of arguments to the function by calling getArgumentCount().

Parameters:

n - an integer index for the argument sought.

Returns:

the nth argument (bound variable) passed to this FunctionDefinition.

getArgument

public ASTNode getArgument(java.lang.String name)

Get the argument named name to this FunctionDefinition.

Parameters:

name - the exact name (case-sensitive) of the sought-after argument

Returns:

the argument (bound variable) having the given name, or null if no such argument exists.

getBody

public ASTNode getBody()

Get the mathematical expression that is the body of this FunctionDefinition object.

Returns:

the body of this FunctionDefinition as an Abstract Syntax Tree, or null if no body is defined.

getId

public java.lang.String getId()

Specified by:

getId in interface NamedSBase

Returns:

the id of the element if it is set, an empty string otherwise.

getName

public java.lang.String getName()

Specified by:

getName in interface NamedSBase

Returns:

the name of the element if it is set, an empty string otherwise.

getNumArguments

public int getNumArguments()

Get the number of arguments (bound variables) taken by this FunctionDefinition.

Returns:

the number of arguments (bound variables) that must be passed to this FunctionDefinition.

getArgumentCount

public int getArgumentCount()

Get the number of arguments (bound variables) taken by this FunctionDefinition.

Returns:

the number of arguments (bound variables) that must be passed to this FunctionDefinition.

getParent

public ListOf<FunctionDefinition> 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()

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()

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: NamedSBase

This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

Returns:

true if the identifier of this element must be set in order to create a valid SBML representation. false otherwise, i.e., if the identifier can be understood as an optional attribute.

isSetId

public boolean isSetId()

Specified by:

isSetId in interface NamedSBase

Returns:

true if the id is not null.

isSetName

public boolean isSetName()

Specified by:

isSetName in interface NamedSBase

Returns:

true if the name 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.

setId

public void setId(java.lang.String id)

Description copied from interface: NamedSBase

sets the id value with 'id'

Specified by:

setId in interface NamedSBase

setMath

public void setMath(ASTNode math)

Description copied from interface: MathContainer

Sets the math ASTNode of this MathContainer to the given value.

Specified by:

setMath in interface MathContainer

Overrides:

setMath in class AbstractMathContainer

Parameters:

math - an abstract syntax tree.

setName

public void setName(java.lang.String name)

Description copied from interface: NamedSBase

sets the name value with 'name'. If level is 1, sets automatically the id to 'name'

Specified by:

setName in interface NamedSBase

toString

public java.lang.String toString()

Overrides:

toString in class AbstractMathContainer

unsetId

public void unsetId()

Description copied from interface: NamedSBase

sets the id value to null.

Specified by:

unsetId in interface NamedSBase

unsetName

public void unsetName()

Description copied from interface: NamedSBase

sets the name value to null.

Specified by:

unsetName in interface NamedSBase

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.