org.sbml.jsbml.math

Class ASTFunction

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.math.AbstractASTNode

org.sbml.jsbml.math.ASTFunction

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, ASTNode2, TreeNodeWithChangeSupport

Direct Known Subclasses:

ASTArithmeticOperatorNode, ASTBinaryFunctionNode, ASTCiFunctionNode, ASTLambdaFunctionNode, ASTLogicalOperatorNode, ASTPiecewiseFunctionNode, ASTQualifierNode, ASTRelationalOperatorNode, ASTUnaryFunctionNode

public class ASTFunction
extends AbstractASTNode

An Abstract Syntax Tree (AST) node representing a function in a mathematical expression.

Since:

1.0

Version:

$Rev$

Author:

Victor Kofia

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.List<ASTNode2>	listOfNodes Child nodes.
private static org.apache.log4j.Logger	logger A Logger for this class.
private java.lang.String	name The name of the MathML element represented by this ASTFunction.
private static long	serialVersionUID

Fields inherited from class org.sbml.jsbml.math.AbstractASTNode

id, mathMLClass, parentSBMLObject, strict, style, type

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
ASTFunction() Creates a new ASTFunction that lacks a pointer to its containing MathContainer.
ASTFunction(ASTFunction other) Copy constructor; Creates a deep copy of the given ASTFunction.
ASTFunction(MathContainer container) Creates a new ASTFunction with a pointer to the specified MathContainer.

Method Summary

Modifier and Type	Method and Description
void	addChild(ASTNode2 child) Adds a child to this node.
ASTFunction	clone() Clone ASTNode2
ASTNode2Value<?>	compile(ASTNode2Compiler compiler) Compiles this ASTNode2 and returns the result.
boolean	equals(java.lang.Object obj)
java.util.List<CallableSBase>	findReferencedCallableSBases() Goes through the formula and identifies all global parameters that are referenced by this rate rule.
boolean	getAllowsChildren()
ASTNode2	getChildAt(int childIndex)
int	getChildCount()
java.util.List<ASTNode2>	getChildren() Returns the list of children of the current ASTFunction.
java.util.List<ASTNode2>	getListOfNodes() Returns the list of children of the current ASTFunction.
java.util.List<ASTNode2>	getListOfNodes(Filter filter) Returns the list of children of the current ASTFunction that satisfy the given filter.
java.lang.String	getName() Returns the name of the MathML element represented by this ASTFunction
int	hashCode()
boolean	hasUnits() Returns true if any one of the descendants of this ASTFunction has a unit defined.
private void	initDefaults() Initializes the default values/attributes of the node.
void	insertChild(int n, ASTNode2 newChild) Inserts the given ASTNode2 at point n in the list of children of this ASTNode2.
boolean	isAllowableType(ASTNode.Type type) Returns true iff type is allowed in this ASTNode2
protected boolean	isSetList() Returns true iff listOfNodes has been set
boolean	isSetName() Returns True iff name has been set
void	prependChild(ASTNode2 child) Adds the given node as a child of this ASTFunction.
boolean	removeChild(int n) Removes child n of this ASTFunction.
ASTNode2	replaceChild(int n, ASTNode2 newChild) Replaces the nth child of this ASTNode2 with the given ASTNode2.
void	setName(java.lang.String name) Set the name of the MathML element represented by this ASTFunction
void	setParentSBMLObject(MathContainer container) Sets the parentSBMLObject to container recursively
void	swapChildren(ASTFunction that) Swaps the children of this ASTFunction with the children of that ASTFunction.

Methods inherited from class org.sbml.jsbml.math.AbstractASTNode

getId, getMathMLClass, getParentSBMLObject, getStyle, getType, isSetId, isSetMathMLClass, isSetParentSBMLObject, isSetStyle, isSetType, isStrict, processValue, setId, setMathMLClass, setParent, setStrictness, setStyle, setType, setType, toFormula, toLaTeX, toMathML, unsetParentSBMLObject

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getParent, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, notifyChildChange, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, toString, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.math.ASTNode2

toString

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, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, getParent, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

logger

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

A Logger for this class.

listOfNodes

protected java.util.List<ASTNode2> listOfNodes

Child nodes.

name

private java.lang.String name

The name of the MathML element represented by this ASTFunction.

Constructor Detail

ASTFunction

public ASTFunction()

Creates a new ASTFunction that lacks a pointer to its containing MathContainer.

ASTFunction

public ASTFunction(ASTFunction other)

Copy constructor; Creates a deep copy of the given ASTFunction.

Parameters:

other - the ASTFunction to be copied.

ASTFunction

public ASTFunction(MathContainer container)

Creates a new ASTFunction with a pointer to the specified MathContainer.

Parameters:

container -

Method Detail

addChild

public void addChild(ASTNode2 child)

Adds a child to this node.

Parameters:

child - the node to add as child.

Throws:

java.lang.NullPointerException - if the child is null

clone

public ASTFunction clone()

Description copied from interface: ASTNode2

Clone ASTNode2

Specified by:

clone in interface ASTNode2

Specified by:

clone in class AbstractASTNode

Returns:

ASTNode2 node

compile

public ASTNode2Value<?> compile(ASTNode2Compiler compiler)

Description copied from interface: ASTNode2

Compiles this ASTNode2 and returns the result.

Parameters:

compiler - An instance of an ASTNode2Compiler that provides methods to translate this ASTNode2 into something different.

Returns:

Some value wrapped in an ASTNode2Value. The content of the wrapper depends on the ASTNode2Compiler used to create it. However, this ASTNode2 will ensure that level and version are set appropriately according to this node's parent SBML object.

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class AbstractASTNode

findReferencedCallableSBases

public java.util.List<CallableSBase> findReferencedCallableSBases()

Goes through the formula and identifies all global parameters that are referenced by this rate rule. Returns empty list if no parameters have been referenced.

Returns:

all global parameters that are referenced by this rate rule.

getAllowsChildren

public boolean getAllowsChildren()

getChildAt

public ASTNode2 getChildAt(int childIndex)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Specified by:

getChildAt in class AbstractASTNode

getChildCount

public int getChildCount()

getChildren

public java.util.List<ASTNode2> getChildren()

Returns the list of children of the current ASTFunction.

Returns:

the list of children of the current ASTFunction.

getListOfNodes

public java.util.List<ASTNode2> getListOfNodes()

Returns the list of children of the current ASTFunction.

Returns:

the list of children of the current ASTFunction.

getListOfNodes

public java.util.List<ASTNode2> getListOfNodes(Filter filter)

Returns the list of children of the current ASTFunction that satisfy the given filter.

Parameters:

filter -

Returns:

the list of children of the current ASTFunction that satisfy the given filter.

getName

public java.lang.String getName()

Returns the name of the MathML element represented by this ASTFunction

Returns:

String name

hashCode

public int hashCode()

Overrides:

hashCode in class AbstractASTNode

hasUnits

public boolean hasUnits()

Returns true if any one of the descendants of this ASTFunction has a unit defined.

Returns:

true

initDefaults

private void initDefaults()

Initializes the default values/attributes of the node.

insertChild

public void insertChild(int n,
                        ASTNode2 newChild)

Inserts the given ASTNode2 at point n in the list of children of this ASTNode2. Inserting a child within an ASTNode2 may result in an inaccurate representation.

Parameters:

n - long the index of the ASTNode2 being added

newChild - ASTNode2 to insert as the n^th child

Throws:

java.lang.NullPointerException - if the child is null

isAllowableType

public boolean isAllowableType(ASTNode.Type type)

Description copied from interface: ASTNode2

Returns true iff type is allowed in this ASTNode2

Returns:

isSetList

protected boolean isSetList()

Returns true iff listOfNodes has been set

Returns:

boolean

isSetName

public boolean isSetName()

Returns True iff name has been set

Returns:

boolean

prependChild

public void prependChild(ASTNode2 child)

Adds the given node as a child of this ASTFunction. This method adds child nodes from right to left.

Parameters:

child - an ASTNode2

Throws:

java.lang.NullPointerException - if the child is null

removeChild

public boolean removeChild(int n)

Removes child n of this ASTFunction. Removing a child from an ASTFunction may result in an inaccurate representation.

Parameters:

n - the index of the child to remove

Returns:

boolean indicating the success or failure of the operation

replaceChild

public ASTNode2 replaceChild(int n,
                             ASTNode2 newChild)

Replaces the n^th child of this ASTNode2 with the given ASTNode2.

Parameters:

n - long the index of the child to replace

newChild - ASTNode2 to replace the n^th child

Returns:

the element previously at the specified position or null if element in question is non-existent

setName

public void setName(java.lang.String name)

Set the name of the MathML element represented by this ASTFunction

Parameters:

name -

setParentSBMLObject

public void setParentSBMLObject(MathContainer container)

Description copied from interface: ASTNode2

Sets the parentSBMLObject to container recursively

Specified by:

setParentSBMLObject in interface ASTNode2

Overrides:

setParentSBMLObject in class AbstractASTNode

swapChildren

public void swapChildren(ASTFunction that)

Swaps the children of this ASTFunction with the children of that ASTFunction.

Unfortunately, when swapping child nodes, we have to recursively traverse the entire subtrees in order to make sure that all pointers to the parent SBML object are correct. However, this must only be done if the parent SBML object of that differs from the one surrounding this node.

In any case, the pointer from each sub-node to its parent must be changed. In contrast to other SBML elements, ASTFunctions have sub-nodes as direct children, i.e., there is no child called 'ListOfNodes'. The setParent method is also not recursive.

However, this might cause many calls to listeners.

Parameters:

that - the other node whose children should be used to replace this node's children