org.sbml.jsbml.math

Class AbstractASTNode

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.math.AbstractASTNode

All Implemented Interfaces:

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

Direct Known Subclasses:

ASTBoolean, ASTFunction, ASTNumber

public abstract class AbstractASTNode
extends AbstractTreeNode
implements ASTNode2

A node in the Abstract Syntax Tree (AST) representation of 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.lang.String	id The style of this MathML element
private static org.apache.log4j.Logger	logger A Logger for this class.
protected java.lang.String	mathMLClass class attribute for MathML element
protected MathContainer	parentSBMLObject The container that holds this AbstractASTNode.
private static long	serialVersionUID
protected boolean	strict Specifies strictness.
protected java.lang.String	style The style of this MathML element
protected ASTNode.Type	type The type of this node

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
AbstractASTNode() Creates an empty AbstractTreeNode without a pointer to its containing MathContainer.
AbstractASTNode(ASTNode2 ast) Constructor for cloning AbstractTreeNode
AbstractASTNode(MathContainer container) Creates an empty AbstractTreeNode with a pointer to the specified MathContainer.

Method Summary

Modifier and Type	Method and Description
abstract ASTNode2	clone() Clone ASTNode2
boolean	equals(java.lang.Object obj)
abstract ASTNode2	getChildAt(int childIndex)
java.lang.String	getId() Get the id of this node
java.lang.String	getMathMLClass() Returns the class of the MathML element represented by this ASTNode2
MathContainer	getParentSBMLObject() Return the parentSBMLObject of this ASTNode2
java.lang.String	getStyle() Return the style of this node
ASTNode.Type	getType() Returns the type of this ASTNode2.
int	hashCode()
boolean	isSetId() Returns true iff id has been set
boolean	isSetMathMLClass() Returns true iff mathMLClass has been set
boolean	isSetParentSBMLObject() Checks if a parent SBML object, i.e., a MathContainer, is set as a parent SBML object for this ASTNode2.
boolean	isSetStyle() Returns true iff style has been set
boolean	isSetType() Returns true iff type has been set
boolean	isStrict() Specifies strictness.
protected ASTNode2Value<?>	processValue(ASTNode2Value<?> value) Set the type, level and version of the specified ASTNode2Value value.
void	setId(java.lang.String id) Set the id of this node
void	setMathMLClass(java.lang.String mathMLClass) Set the class of the MathML element represented by this ASTNode2
void	setParent(javax.swing.tree.TreeNode parent)
void	setParentSBMLObject(MathContainer container) Sets the parentSBMLObject to container recursively
void	setStrictness(boolean strict) Set the strictness of this node
void	setStyle(java.lang.String style) Set the style of this node
void	setType(ASTNode.Type type) Set the type of the MathML element represented by this ASTNode2
void	setType(java.lang.String typeStr) Sets the type from a String.
java.lang.String	toFormula() Converts this ASTNode2 to a text string using a specific syntax for mathematical formulas.
java.lang.String	toLaTeX() Converts this node recursively into a LaTeX formatted String.
java.lang.String	toMathML() Converts this node recursively into a MathML string that corresponds to the subset of MathML defined in the SBML specification.
void	unsetParentSBMLObject() Unsets the parentSBMLObject to null recursively.

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, wait, wait, wait

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

compile, isAllowableType, 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, getAllowsChildren, getChildCount, 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.

parentSBMLObject

protected MathContainer parentSBMLObject

The container that holds this AbstractASTNode.

strict

protected boolean strict

Specifies strictness. When true, ASTUnaryFunction and ASTBinaryFunction nodes can only contain the specified # of children. When false, there is a bit of leeway (i.e. ASTUnaryFunction can contain more than one child) (not recommended).

type

protected ASTNode.Type type

The type of this node

id

protected java.lang.String id

The style of this MathML element

style

protected java.lang.String style

The style of this MathML element

mathMLClass

protected java.lang.String mathMLClass

class attribute for MathML element

Constructor Detail

AbstractASTNode

public AbstractASTNode()

Creates an empty AbstractTreeNode without a pointer to its containing MathContainer.

AbstractASTNode

public AbstractASTNode(ASTNode2 ast)

Constructor for cloning AbstractTreeNode

Parameters:

ast -

AbstractASTNode

public AbstractASTNode(MathContainer container)

Creates an empty AbstractTreeNode with a pointer to the specified MathContainer.

Parameters:

container -

Method Detail

clone

public abstract ASTNode2 clone()

Description copied from interface: ASTNode2

Clone ASTNode2

Specified by:

clone in interface ASTNode2

Specified by:

clone in class AbstractTreeNode

Returns:

ASTNode2 node

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class AbstractTreeNode

getChildAt

public abstract ASTNode2 getChildAt(int childIndex)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

getId

public java.lang.String getId()

Description copied from interface: ASTNode2

Get the id of this node

Specified by:

getId in interface ASTNode2

Returns:

the id

getMathMLClass

public java.lang.String getMathMLClass()

Description copied from interface: ASTNode2

Returns the class of the MathML element represented by this ASTNode2

Specified by:

getMathMLClass in interface ASTNode2

Returns:

String name

getParentSBMLObject

public MathContainer getParentSBMLObject()

Description copied from interface: ASTNode2

Return the parentSBMLObject of this ASTNode2

Specified by:

getParentSBMLObject in interface ASTNode2

Returns:

MathContainer container

getStyle

public java.lang.String getStyle()

Description copied from interface: ASTNode2

Return the style of this node

Specified by:

getStyle in interface ASTNode2

Returns:

the style

getType

public ASTNode.Type getType()

Description copied from interface: ASTNode2

Returns the type of this ASTNode2.

Specified by:

getType in interface ASTNode2

Returns:

Type type

hashCode

public int hashCode()

Overrides:

hashCode in class AbstractTreeNode

isSetId

public boolean isSetId()

Description copied from interface: ASTNode2

Returns true iff id has been set

Specified by:

isSetId in interface ASTNode2

Returns:

boolean

isSetMathMLClass

public boolean isSetMathMLClass()

Description copied from interface: ASTNode2

Returns true iff mathMLClass has been set

Specified by:

isSetMathMLClass in interface ASTNode2

Returns:

boolean

isSetParentSBMLObject

public boolean isSetParentSBMLObject()

Description copied from interface: ASTNode2

Checks if a parent SBML object, i.e., a MathContainer, is set as a parent SBML object for this ASTNode2.

Specified by:

isSetParentSBMLObject in interface ASTNode2

Returns:

boolean

isSetStyle

public boolean isSetStyle()

Description copied from interface: ASTNode2

Returns true iff style has been set

Specified by:

isSetStyle in interface ASTNode2

Returns:

boolean

isSetType

public boolean isSetType()

Description copied from interface: ASTNode2

Returns true iff type has been set

Specified by:

isSetType in interface ASTNode2

Returns:

boolean

isStrict

public boolean isStrict()

Description copied from interface: ASTNode2

Specifies strictness. When true, ASTUnaryFunction and ASTBinaryFunction nodes can only contain the specified # of children. When false, there is a bit of leeway (i.e. ASTUnaryFunction can contain more than one child) (not recommended).

Specified by:

isStrict in interface ASTNode2

Returns:

boolean

processValue

protected ASTNode2Value<?> processValue(ASTNode2Value<?> value)

Set the type, level and version of the specified ASTNode2Value value.

Parameters:

value - ASTNode2Value

Returns:

value ASTNode2Value

setId

public void setId(java.lang.String id)

Description copied from interface: ASTNode2

Set the id of this node

Specified by:

setId in interface ASTNode2

Parameters:

id - the id to set

setMathMLClass

public void setMathMLClass(java.lang.String mathMLClass)

Description copied from interface: ASTNode2

Set the class of the MathML element represented by this ASTNode2

Specified by:

setMathMLClass in interface ASTNode2

setParent

public void setParent(javax.swing.tree.TreeNode parent)

Specified by:

setParent in interface ASTNode2

Overrides:

setParent in class AbstractTreeNode

Parameters:

parent - the parent to set

setParentSBMLObject

public void setParentSBMLObject(MathContainer container)

Description copied from interface: ASTNode2

Sets the parentSBMLObject to container recursively

Specified by:

setParentSBMLObject in interface ASTNode2

setStrictness

public void setStrictness(boolean strict)

Set the strictness of this node

Specified by:

setStrictness in interface ASTNode2

Parameters:

strict -

setStyle

public void setStyle(java.lang.String style)

Description copied from interface: ASTNode2

Set the style of this node

Specified by:

setStyle in interface ASTNode2

Parameters:

style - the style to set

setType

public void setType(java.lang.String typeStr)

Description copied from interface: ASTNode2

Sets the type from a String. This method accepts all the supported mathML elements, the possible types of cn elements or the possible definitionURL of csymbol elements.

Specified by:

setType in interface ASTNode2

Parameters:

typeStr - the type as a String.

setType

public void setType(ASTNode.Type type)

Description copied from interface: ASTNode2

Set the type of the MathML element represented by this ASTNode2

Specified by:

setType in interface ASTNode2

toFormula

public java.lang.String toFormula()
                           throws SBMLException

Description copied from interface: ASTNode2

Converts this ASTNode2 to a text string using a specific syntax for mathematical formulas.

The text-string form of mathematical formulas produced by formulaToString() and read by parseFormula() are simple C-inspired infix notation taken from SBML Level 1. A formula in this text-string form therefore can be handed to a program that understands SBML Level 1 mathematical expressions, or used as part of a formula translation system. The syntax is described in detail in the documentation for ASTNode.

Specified by:

toFormula in interface ASTNode2

Returns:

the formula from the given AST as an SBML Level 1 text-string mathematical formula. The caller owns the returned string and is responsible for freeing it when it is no longer needed. null is returned if the given argument is null.

Throws:

SBMLException - if there is a problem in the ASTNode2 tree.

toLaTeX

public java.lang.String toLaTeX()
                         throws SBMLException

Description copied from interface: ASTNode2

Converts this node recursively into a LaTeX formatted String.

Specified by:

toLaTeX in interface ASTNode2

Returns:

A String representing the LaTeX code necessary to write the formula corresponding to this node in a document.

Throws:

SBMLException - if there is a problem in the AbstractASTNode tree.

toMathML

public java.lang.String toMathML()

Description copied from interface: ASTNode2

Converts this node recursively into a MathML string that corresponds to the subset of MathML defined in the SBML specification.

Specified by:

toMathML in interface ASTNode2

Returns:

the representation of this node in MathML.

unsetParentSBMLObject

public void unsetParentSBMLObject()

Description copied from interface: ASTNode2

Unsets the parentSBMLObject to null recursively.

Specified by:

unsetParentSBMLObject in interface ASTNode2