org.sbml.jsbml.math

Class ASTCiFunctionNode

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.math.AbstractASTNode

org.sbml.jsbml.math.ASTFunction

org.sbml.jsbml.math.ASTCiFunctionNode

All Implemented Interfaces:

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

public class ASTCiFunctionNode
extends ASTFunction
implements ASTCSymbolBaseNode

An Abstract Syntax Tree (AST) node representing a MathML ci element 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
private java.lang.String	definitionURL definitionURL attribute for MathML element
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 ASTCiFunctionNode.
private java.lang.String	refId refId attribute for MathML element
private static long	serialVersionUID

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

listOfNodes

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
ASTCiFunctionNode() Creates a new ASTCiFunctionNode.
ASTCiFunctionNode(ASTCiFunctionNode node) Copy constructor; Creates a deep copy of the given ASTCiFunctionNode.

Method Summary

Modifier and Type	Method and Description
ASTCiFunctionNode	clone() Clone ASTNode2
ASTNode2Value<?>	compile(ASTNode2Compiler compiler) Compiles this ASTNode2 and returns the result.
boolean	equals(java.lang.Object obj)
java.lang.String	getDefinitionURL() Returns the definitionURL of the MathML element represented by this ASTCiFunctionNode
FunctionDefinition	getReferenceInstance() Returns the variable (FunctionDefinition) of this ASTCiFunctionNode.
java.lang.String	getRefId() Get refId attribute
int	hashCode()
boolean	isAllowableType(ASTNode.Type type) Returns true iff type is allowed in this ASTNode2
boolean	isSetDefinitionURL() Returns True iff definitionURL has been set
boolean	isSetRefId() Return true iff refId is set
boolean	isSetType() Returns true iff type has been set
boolean	refersTo(java.lang.String id) Returns true if this node or one of its descendants contains some identifier with the given id.
void	setDefinitionURL(java.lang.String definitionURL) Set the definitionURL of the MathML element represented by this ASTCiFunctionNode
void	setReference(FunctionDefinition function) Set an instance of FunctionDefinition as the variable of this ASTCiFunctionNode.
void	setRefId(java.lang.String refId) Set refId attribute
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.

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

addChild, findReferencedCallableSBases, getAllowsChildren, getChildAt, getChildCount, getChildren, getListOfNodes, getListOfNodes, getName, hasUnits, insertChild, isSetList, isSetName, prependChild, removeChild, replaceChild, setName, setParentSBMLObject, swapChildren

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

getId, getMathMLClass, getParentSBMLObject, getStyle, getType, isSetId, isSetMathMLClass, isSetParentSBMLObject, isSetStyle, isStrict, processValue, setId, setMathMLClass, setParent, setStrictness, setStyle, setType, setType, 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.ASTCSymbolBaseNode

getName, isSetName, setName

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

getId, getMathMLClass, getParentSBMLObject, getStyle, getType, isSetId, isSetMathMLClass, isSetParentSBMLObject, isSetStyle, isStrict, setId, setMathMLClass, setParent, setParentSBMLObject, setStrictness, setStyle, setType, setType, toString, unsetParentSBMLObject

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, getChildAt, getChildCount, getIndex, getParent, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

logger

private static final org.apache.log4j.Logger logger

A Logger for this class.

definitionURL

private java.lang.String definitionURL

definitionURL attribute for MathML element

name

private java.lang.String name

The name of the MathML element represented by this ASTCiFunctionNode.

refId

private java.lang.String refId

refId attribute for MathML element

Constructor Detail

ASTCiFunctionNode

public ASTCiFunctionNode()

Creates a new ASTCiFunctionNode.

ASTCiFunctionNode

public ASTCiFunctionNode(ASTCiFunctionNode node)

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

Parameters:

node - the ASTCiFunctionNode to be copied.

Method Detail

clone

public ASTCiFunctionNode clone()

Description copied from interface: ASTNode2

Clone ASTNode2

Specified by:

clone in interface ASTNode2

Overrides:

clone in class ASTFunction

Returns:

ASTNode2 node

compile

public ASTNode2Value<?> compile(ASTNode2Compiler compiler)

Description copied from interface: ASTNode2

Compiles this ASTNode2 and returns the result.

Specified by:

compile in interface ASTNode2

Overrides:

compile in class ASTFunction

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 ASTFunction

getDefinitionURL

public java.lang.String getDefinitionURL()

Returns the definitionURL of the MathML element represented by this ASTCiFunctionNode

Specified by:

getDefinitionURL in interface ASTCSymbolBaseNode

Returns:

String definitionURL

getReferenceInstance

public FunctionDefinition getReferenceInstance()

Returns the variable (FunctionDefinition) of this ASTCiFunctionNode.

Returns:

the variable of this node

getRefId

public java.lang.String getRefId()

Get refId attribute

Returns:

the refId

hashCode

public int hashCode()

Overrides:

hashCode in class ASTFunction

isAllowableType

public boolean isAllowableType(ASTNode.Type type)

Description copied from interface: ASTNode2

Returns true iff type is allowed in this ASTNode2

Specified by:

isAllowableType in interface ASTNode2

Overrides:

isAllowableType in class ASTFunction

Returns:

isSetDefinitionURL

public boolean isSetDefinitionURL()

Description copied from interface: ASTCSymbolBaseNode

Returns True iff definitionURL has been set

Specified by:

isSetDefinitionURL in interface ASTCSymbolBaseNode

Returns:

boolean

isSetRefId

public boolean isSetRefId()

Return true iff refId is set

Returns:

boolean

isSetType

public boolean isSetType()

Description copied from interface: ASTNode2

Returns true iff type has been set

Specified by:

isSetType in interface ASTNode2

Overrides:

isSetType in class AbstractASTNode

Returns:

boolean

refersTo

public boolean refersTo(java.lang.String id)

Description copied from interface: ASTCSymbolBaseNode

Returns true if this node or one of its descendants contains some identifier with the given id. This method can be used to scan a formula for a specific parameter or species and detect whether this component is used by this formula. This search is done using a DFS.

Specified by:

refersTo in interface ASTCSymbolBaseNode

Parameters:

id - the id of an SBML element.

Returns:

true if this node or one of its descendants contains the given id.

setDefinitionURL

public void setDefinitionURL(java.lang.String definitionURL)

Set the definitionURL of the MathML element represented by this ASTCiFunctionNode

Parameters:

definitionURL -

setReference

public void setReference(FunctionDefinition function)

Set an instance of FunctionDefinition as the variable of this ASTCiFunctionNode. Note that if the given variable does not have a declared id field, the pointer to this variable will get lost when cloning this node. Only references to identifiers are permanently stored. The pointer can also not be written to an SBML file without a valid identifier.

Parameters:

function - a pointer to a FunctionDefinition.

setRefId

public void setRefId(java.lang.String refId)

Set refId attribute

Parameters:

refId - the refId to set

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

Overrides:

toFormula in class AbstractASTNode

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

Overrides:

toLaTeX in class AbstractASTNode

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

Overrides:

toMathML in class AbstractASTNode

Returns:

the representation of this node in MathML.