libSBML C++ API  libSBML 5.19.0 C++ API
ASTNode Class Reference

Detailed Description

@sbmlpackage{core}

Abstract Syntax Tree (AST) representation of a mathematical expression.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

Abstract Syntax Trees (ASTs) are a simple kind of data structure used in libSBML for storing mathematical expressions. The ASTNode is the cornerstone of libSBML's AST representation. An AST "node" represents the most basic, indivisible part of a mathematical formula and come in many types. For instance, there are node types to represent numbers (with subtypes to distinguish integer, real, and rational numbers), names (e.g., constants or variables), simple mathematical operators, logical or relational operators and functions. LibSBML ASTs provide a canonical, in-memory representation for all mathematical formulas regardless of their original format (which might be MathML or might be text strings).

ASTNodeType_t

Converting between ASTs and text strings

The text-string form of mathematical formulas produced by SBML_formulaToString()

Examples
createExampleSBML.cpp, printMath.cpp, qual_example1.cpp, translateL3Math.cpp, and translateMath.cpp.

Public Member Functions

int addChild (ASTNode *disownedChild, bool inRead=false)
 Adds the given node as a child of this ASTNode. More...
 
int addSemanticsAnnotation (XMLNode *disownedAnnotation)
 Adds the given XMLNode as a MathML <semantics> element to this ASTNode. More...
 
 ASTNode (ASTNodeType_t type=AST_UNKNOWN)
 Creates and returns a new ASTNode. More...
 
 ASTNode (const ASTNode &orig)
 Copy constructor; creates a deep copy of the given ASTNode. More...
 
 ASTNode (Token_t *token)
 Creates a new ASTNode from the given Token. More...
 
bool canonicalize ()
 Converts this ASTNode to a canonical form and returns true if successful, false otherwise. More...
 
ASTNodedeepCopy () const
 Creates a recursive copy of this node and all its children. More...
 
void fillListOfNodes (ASTNodePredicate predicate, List *lst) const
 Returns a list of nodes rooted at a given node and satisfying a given predicate. More...
 
int freeName ()
 Frees the name of this ASTNode and sets it to NULL. More...
 
ASTBasePlugin * getASTPlugin (ASTNodeType_t type)
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension for the package that defines the given type. More...
 
const ASTBasePlugin * getASTPlugin (ASTNodeType_t type) const
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension for the package that defines the given type. More...
 
ASTBasePlugin * getASTPlugin (const SBMLNamespaces *sbmlns)
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given sbmlns. More...
 
const ASTBasePlugin * getASTPlugin (const SBMLNamespaces *sbmlns) const
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given sbmlns. More...
 
ASTBasePlugin * getASTPlugin (const std::string &name, bool isCsymbol=false, bool strCmpIsCaseSensitive=false)
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension for the package with the given constraints. More...
 
const ASTBasePlugin * getASTPlugin (const std::string &name, bool isCsymbol=false, bool strCmpIsCaseSensitive=false) const
 Returns a plug-in object (extension interface) for an SBML Level 3 package extension for the package with the given constraints. More...
 
char getCharacter () const
 Returns the value of this node as a single character. More...
 
ASTNodegetChild (unsigned int n) const
 Returns the child at index n of this node. More...
 
std::string getClass () const
 Returns the MathML class attribute value of this ASTNode. More...
 
XMLAttributesgetDefinitionURL () const
 Returns the MathML definitionURL attribute value. More...
 
std::string getDefinitionURLString () const
 Returns the MathML definitionURL attribute value as a string. More...
 
long getDenominator () const
 Returns the value of the denominator of this node. More...
 
long getExponent () const
 Returns the exponent value of this ASTNode. More...
 
std::string getId () const
 Returns the MathML id attribute value of this ASTNode. More...
 
long getInteger () const
 Returns the value of this node as an integer. More...
 
ASTNodegetLeftChild () const
 Returns the left child of this node. More...
 
ListgetListOfNodes (ASTNodePredicate predicate) const
 Returns a list of nodes satisfying a given predicate. More...
 
double getMantissa () const
 Returns the mantissa value of this node. More...
 
const char * getName () const
 Returns the value of this node as a string. More...
 
unsigned int getNumChildren () const
 Returns the number of children of this node. More...
 
long getNumerator () const
 Returns the value of the numerator of this node if of type AST_RATIONALendif. More...
 
unsigned int getNumSemanticsAnnotations () const
 Returns the number of MathML <semantics> element elements on this node. More...
 
const char * getOperatorName () const
 Returns the value of this operator node as a string. More...
 
SBasegetParentSBMLObject () const
 Returns the parent SBML object. More...
 
int getPrecedence () const
 Returns the precedence of this node in the infix math syntax of SBML Level 1. More...
 
double getReal () const
 Returns the real-numbered value of this node. More...
 
ASTNodegetRightChild () const
 Returns the right child of this node. More...
 
XMLNodegetSemanticsAnnotation (unsigned int n) const
 Returns the nth MathML <semantics> element on this ASTNode. More...
 
std::string getStyle () const
 Returns the MathML style attribute value of this ASTNode. More...
 
ASTNodeType_t getType () const
 Returns the type of this ASTNode. More...
 
std::string getUnits () const
 Returns the units of this ASTNode. More...
 
void * getUserData () const
 Returns the user data that has been previously set via setUserData(). More...
 
double getValue () const
 Returns the numerical value of this ASTNode. More...
 
bool hasCorrectNumberArguments () const
 Returns true if this ASTNode has the correct number of children for its type. More...
 
int hasTypeAndNumChildren (ASTNodeType_t type, unsigned int numchildren) const
 Returns true if this node is of type type and has numchildren number of children. More...
 
bool hasUnits () const
 Returns true (nonzero) if this node or any of its children nodes have the attribute sbml:units. More...
 
int insertChild (unsigned int n, ASTNode *disownedChild)
 Inserts the given ASTNode at point n in the list of children of this ASTNode. More...
 
bool isAvogadro () const
 Returns true (nonzero) if this node is the special symbol avogadro. More...
 
bool isBoolean () const
 Returns true if this node has a Boolean type. More...
 
bool isCiNumber () const
 Returns true (nonzero) if this node represents a MathML ci element representing a value not a function (e.g., true, Pi). More...
 
bool isConstant () const
 Returns true (nonzero) if this node represents a MathML constant (e.g., true, Pi). More...
 
bool isConstantNumber () const
 Returns true (nonzero) if this node represents a MathML constant with numeric value (e.g., Pi). More...
 
bool isCSymbolFunction () const
 Returns true (nonzero) if this node represents a MathML csymbol representing a function. More...
 
bool isFunction () const
 Returns true if this node represents a function. More...
 
bool isInfinity () const
 Returns true (nonzero) if this node represents the special IEEE 754 value infinity, false (zero) otherwise. More...
 
bool isInteger () const
 Returns true (nonzero) if this node contains an integer value, false (zero) otherwise. More...
 
bool isLambda () const
 Returns true (nonzero) if this node is a MathML <lambda>, false (zero) otherwise. More...
 
bool isLog10 () const
 Returns true (nonzero) if this node represents a log10 function, false (zero) otherwise. More...
 
bool isLogical () const
 Returns true (nonzero) if this node is a MathML logical operator. More...
 
bool isName () const
 Returns true if this node is a user-defined variable name or the symbols for time or Avogadro's constant. More...
 
bool isNaN () const
 Returns true (nonzero) if this node represents the special IEEE 754 value "not a number" (NaN), false (zero) otherwise. More...
 
bool isNegInfinity () const
 Returns true (nonzero) if this node represents the special IEEE 754 value "negative infinity", false (zero) otherwise. More...
 
bool isNumber () const
 Returns true (nonzero) if this node contains a number, false (zero) otherwise. More...
 
bool isOperator () const
 Returns true if this node is a mathematical operator. More...
 
bool isPiecewise () const
 Returns true (nonzero) if this node is the MathML <piecewise> construct. More...
 
bool isRational () const
 Returns true (nonzero) if this node represents a rational number. More...
 
bool isReal () const
 Returns true (nonzero) if this node can represent a real number, false (zero) otherwise. More...
 
bool isRelational () const
 Returns true if this node is a MathML relational operator. More...
 
bool isSetClass () const
 Returns true (nonzero) if this node has a value for the MathML attribute "class". More...
 
bool isSetId () const
 Returns true (nonzero) if this node has a value for the MathML attribute "id". More...
 
bool isSetParentSBMLObject () const
 Returns true if this node has a value for the parent SBML object. More...
 
bool isSetStyle () const
 Returns true (nonzero) if this node has a value for the MathML attribute "style". More...
 
bool isSetUnits () const
 Returns true (nonzero) if this node has the attribute sbml:units. More...
 
bool isSetUserData () const
 Returns true if this node has a user data object. More...
 
bool isSqrt () const
 Returns true (nonzero) if this node represents a square root function, false (zero) otherwise. More...
 
bool isUMinus () const
 Returns true (nonzero) if this node is a unary minus operator, false (zero) otherwise. More...
 
bool isUnknown () const
 Returns true (nonzero) if this node has an unknown type. More...
 
bool isUPlus () const
 Returns true (nonzero) if this node is a unary plus operator, false (zero) otherwise. More...
 
bool isUserFunction () const
 Returns true (nonzero) if this node represents a MathML user-defined function. More...
 
bool isWellFormedASTNode () const
 Returns true or false depending on whether this ASTNode is well-formed. More...
 
ASTNodeoperator= (const ASTNode &rhs)
 Assignment operator for ASTNode. More...
 
int prependChild (ASTNode *disownedChild)
 Adds the given node as a child of this ASTNode. More...
 
void reduceToBinary ()
 Reduces this ASTNode to a binary tree. More...
 
int removeChild (unsigned int n)
 Removes the nth child of this ASTNode object. More...
 
virtual void renameSIdRefs (const std::string &oldid, const std::string &newid)
 Renames all the SIdRef attributes on this node and any child node. More...
 
virtual void renameUnitSIdRefs (const std::string &oldid, const std::string &newid)
 Renames all the UnitSIdRef attributes on this node and any child node. More...
 
void replaceArgument (const std::string &bvar, ASTNode *arg)
 Replaces occurrences of a given name with a given ASTNode. More...
 
int replaceChild (unsigned int n, ASTNode *disownedChild, bool delreplaced=false)
 Replaces and optionally deletes the nth child of this ASTNode with the given ASTNode. More...
 
bool returnsBoolean (const Model *model=NULL) const
 Returns true (nonzero) if this node returns a Boolean type or false (zero) otherwise. More...
 
int setCharacter (char value)
 Sets the value of this ASTNode to the given character. More...
 
int setClass (const std::string &className)
 Sets the MathML attribute class of this ASTNode to className. More...
 
int setId (const std::string &id)
 Sets the MathML attribute id of this ASTNode. More...
 
int setName (const char *name)
 Sets the value of this ASTNode to the given name. More...
 
int setStyle (const std::string &style)
 Sets the MathML attribute style of this ASTNode to style. More...
 
int setType (ASTNodeType_t type)
 Sets the type of this ASTNode to the given type code. More...
 
int setUnits (const std::string &units)
 Sets the units of this ASTNode to units. More...
 
int setUserData (void *userData)
 Sets the user data of this node. More...
 
int setValue (double mantissa, long exponent)
 Sets the value of this ASTNode to the given real (double) in two parts: the mantissa and the exponent. More...
 
int setValue (double value)
 Sets the value of this ASTNode to the given real (double) and sets the node type to AST_REALendif. More...
 
int setValue (int value)
 Sets the value of this ASTNode to the given integer and sets the node type to AST_INTEGERendif. More...
 
int setValue (long numerator, long denominator)
 Sets the value of this ASTNode to the given rational in two parts: the numerator and denominator. More...
 
int setValue (long value)
 Sets the value of this ASTNode to the given (long) integer and sets the node type to AST_INTEGERendif. More...
 
int swapChildren (ASTNode *that)
 Swaps the children of this ASTNode object with the children of the given ASTNode object. More...
 
int unsetClass ()
 Unsets the MathML class attribute of this ASTNode. More...
 
int unsetId ()
 Unsets the MathML id attribute of this ASTNode. More...
 
int unsetParentSBMLObject ()
 Unsets the parent SBML object. More...
 
int unsetStyle ()
 Unsets the MathML style attribute of this ASTNode. More...
 
int unsetUnits ()
 Unsets the units of this ASTNode. More...
 
int unsetUserData ()
 Unsets the user data of this node. More...
 
virtual ~ASTNode ()
 Destroys this ASTNode, including any child nodes. More...
 

Constructor & Destructor Documentation

◆ ASTNode() [1/3]

ASTNode::ASTNode ( ASTNodeType_t  type = AST_UNKNOWN)

Creates and returns a new ASTNode.

Unless the argument type is given, the returned node will by default have a type of AST_UNKNOWNendif

◆ ASTNode() [2/3]

ASTNode::ASTNode ( Token_t token)

Creates a new ASTNode from the given Token.

The resulting ASTNode will contain the same data as the token.

Parameters
tokenthe token to use as a starting point for creating the ASTNode object.

◆ ASTNode() [3/3]

ASTNode::ASTNode ( const ASTNode orig)

Copy constructor; creates a deep copy of the given ASTNode.

Parameters
origthe ASTNode to be copied.

◆ ~ASTNode()

ASTNode::~ASTNode ( )
virtual

Destroys this ASTNode, including any child nodes.

Member Function Documentation

◆ addChild()

int ASTNode::addChild ( ASTNode disownedChild,
bool  inRead = false 
)

Adds the given node as a child of this ASTNode.

Child nodes are added in-order, from left to right.

Parameters
disownedChildthe ASTNode instance to add.
inReadfalse by default; may be set to true when reading XML where there may be a lambda function with no bvar arguments.
Examples
createExampleSBML.cpp.

◆ addSemanticsAnnotation()

int ASTNode::addSemanticsAnnotation ( XMLNode disownedAnnotation)

Adds the given XMLNode as a MathML <semantics> element to this ASTNode.

The <semantics> element is a MathML 2.0 construct that can be used to associate additional information with a MathML construct. The construct can be used to decorate a MathML expressions with a sequence of one or more <annotation> or <annotation-xml> elements. Each such element contains a pair of items; the first is a symbol that acts as an attribute or key, and the second is the value associated with the attribute or key. Please refer to the MathML 2.0 documentation, particularly the Section 5.2, Semantic Annotations for more information about these constructs.
Parameters
disownedAnnotationthe annotation to add. Will become a child of the parent node.

◆ canonicalize()

bool ASTNode::canonicalize ( )

Converts this ASTNode to a canonical form and returns true if successful, false otherwise.

The rules determining the canonical form conversion are as follows:

◆ deepCopy()

ASTNode * ASTNode::deepCopy ( ) const

Creates a recursive copy of this node and all its children.

Returns
a copy of this ASTNode and all its children. The caller owns the returned ASTNode and is responsible for deleting it.

◆ fillListOfNodes()

void ASTNode::fillListOfNodes ( ASTNodePredicate  predicate,
List lst 
) const

Returns a list of nodes rooted at a given node and satisfying a given predicate.

This method is identical to calling getListOfNodes(ASTNodePredicate predicate) const, except that instead of creating a new List object, it uses the one passed in as argument lst. This method a depth-first search of the tree rooted at this ASTNode object, and adds to the list lst the nodes for which the given function predicate(node) returns true (nonzero).

For portability between different programming languages, the predicate is passed in as a pointer to a function. The function definition must have the type ASTNodePredicate , which is defined as

int (*ASTNodePredicate) (const ASTNode_t *node);

where a return value of nonzero represents true and zero represents false.

Parameters
predicatethe predicate to use.
lstthe List to which ASTNode objects should be added.
See also
getListOfNodes()

◆ freeName()

int ASTNode::freeName ( )

Frees the name of this ASTNode and sets it to NULL.

This operation is only applicable to ASTNode objects corresponding to operators, numbers, or AST_UNKNOWNendif

◆ getASTPlugin() [1/6]

ASTBasePlugin* ASTNode::getASTPlugin ( ASTNodeType_t  type)

Returns a plug-in object (extension interface) for an SBML Level 3 package extension for the package that defines the given type.

Parameters
typethe ASTNodeType_t that is defined by the given plugin.
Returns
the plug-in object (the libSBML extension interface) of a package extension that defines the given type, or NULL if none exist.

◆ getASTPlugin() [2/6]

const ASTBasePlugin* ASTNode::getASTPlugin ( ASTNodeType_t  type) const

Returns a plug-in object (extension interface) for an SBML Level 3 package extension for the package that defines the given type.

Parameters
typethe ASTNodeType_t that is defined by the given plugin.
Returns
the plug-in object (the libSBML extension interface) of a package extension that defines the given type, or NULL if none exist.

◆ getASTPlugin() [3/6]

ASTBasePlugin* ASTNode::getASTPlugin ( const SBMLNamespaces sbmlns)

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given sbmlns.

Parameters
sbmlnsthe namespace of the plugin to return.
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI, or NULL if none exist.

◆ getASTPlugin() [4/6]

const ASTBasePlugin* ASTNode::getASTPlugin ( const SBMLNamespaces sbmlns) const

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given sbmlns.

Parameters
sbmlnsthe namespace of the plugin to return.
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI, or NULL if none exist.

◆ getASTPlugin() [5/6]

ASTBasePlugin* ASTNode::getASTPlugin ( const std::string &  name,
bool  isCsymbol = false,
bool  strCmpIsCaseSensitive = false 
)

Returns a plug-in object (extension interface) for an SBML Level 3 package extension for the package with the given constraints.

Parameters
namethe type or csymbol defined by the returned plugin.
isCsymbolBoolean indicator of whether the name is a csymbol (if true) or type (if false).
strCmpIsCaseSensitivewhether to search for the matching type or csymbol in case-sensitve manner (if true) or case-insensitive manner (if false).
Returns
the plug-in object (the libSBML extension interface) of a package extension that defines the given name, or NULL if none exist.

◆ getASTPlugin() [6/6]

const ASTBasePlugin* ASTNode::getASTPlugin ( const std::string &  name,
bool  isCsymbol = false,
bool  strCmpIsCaseSensitive = false 
) const

Returns a plug-in object (extension interface) for an SBML Level 3 package extension for the package with the given constraints.

Parameters
namethe type or csymbol defined by the returned plugin.
isCsymbolBoolean indicator of whether the name is a csymbol (if true) or type (if false).
strCmpIsCaseSensitivewhether to search for the matching type or csymbol in case-sensitve manner (if true) or case-insensitive manner (if false).
Returns
the plug-in object (the libSBML extension interface) of a package extension that defines the given name, or NULL if none exist.

◆ getCharacter()

char ASTNode::getCharacter ( ) const

Returns the value of this node as a single character.

This function should be called only when getType() returns AST_PLUSendif

◆ getChild()

ASTNode * ASTNode::getChild ( unsigned int  n) const

Returns the child at index n of this node.

Parameters
nthe index of the child to get.
Returns
the nth child of this ASTNode or NULL if this node has no nth child (n > getNumChildren() - 1).
See also
getNumChildren()
getLeftChild()
getRightChild()
Examples
printMath.cpp.

◆ getClass()

std::string ASTNode::getClass ( ) const

Returns the MathML class attribute value of this ASTNode.

Returns
the MathML class of this ASTNode, or an empty string if it does not exist.
See also
isSetClass()
setClass()
unsetClass()

◆ getDefinitionURL()

XMLAttributes * ASTNode::getDefinitionURL ( ) const

Returns the MathML definitionURL attribute value.

Returns
the value of the definitionURL attribute, in the form of a libSBML XMLAttributes object.
See also
setDefinitionURL(XMLAttributes url)
setDefinitionURL(const std::string& url)
getDefinitionURLString()

◆ getDefinitionURLString()

std::string ASTNode::getDefinitionURLString ( ) const

Returns the MathML definitionURL attribute value as a string.

Returns
the value of the definitionURL attribute, as a string.
See also
getDefinitionURL()
setDefinitionURL(const std::string& url)
setDefinitionURL(XMLAttributes url)

◆ getDenominator()

long ASTNode::getDenominator ( ) const

Returns the value of the denominator of this node.

Returns
the value of the denominator of this ASTNode, or 1 (true) if this node is not of type AST_RATIONALendif

◆ getExponent()

long ASTNode::getExponent ( ) const

Returns the exponent value of this ASTNode.

Returns
the value of the exponent of this ASTNode, or 0 if this is not a type of node that has an exponent.
Note
This function should be called only when getType() returns AST_REAL_Eendif

◆ getId()

std::string ASTNode::getId ( ) const

Returns the MathML id attribute value of this ASTNode.

Returns
the MathML id of this ASTNode.
See also
isSetId()
setId(const std::string& id)
unsetId()

◆ getInteger()

long ASTNode::getInteger ( ) const

Returns the value of this node as an integer.

If this node type is AST_RATIONALendif

◆ getLeftChild()

ASTNode * ASTNode::getLeftChild ( ) const

Returns the left child of this node.

Returns
the left child of this ASTNode. This is equivalent to calling getChild() with an argument of 0.
See also
getNumChildren()
getChild()
getRightChild()
Examples
createExampleSBML.cpp, and printMath.cpp.

◆ getListOfNodes()

List * ASTNode::getListOfNodes ( ASTNodePredicate  predicate) const

Returns a list of nodes satisfying a given predicate.

This performs a depth-first search of the tree rooted at this ASTNode object, and returns a List of nodes for which the given function predicate(node) returns true (nonzero).

For portability between different programming languages, the predicate is passed in as a pointer to a function. The function definition must have the type ASTNodePredicate, which is defined as

int (*ASTNodePredicate) (const ASTNode *node);

where a return value of nonzero represents true and zero represents false.

Parameters
predicatethe predicate to use.
Returns
the list of nodes for which the predicate returned true (nonzero). The List returned is owned by the caller and should be deleted after the caller is done using it. The ASTNode objects in the list; however, are not owned by the caller (as they still belong to the tree itself), and therefore should not be deleted.

◆ getMantissa()

double ASTNode::getMantissa ( ) const

Returns the mantissa value of this node.

If getType() returns AST_REALendif

◆ getName()

const char * ASTNode::getName ( ) const

Returns the value of this node as a string.

This function may be called on nodes that (1) are not operators, i.e., nodes for which isOperator() returns false, and (2) are not numbers, i.e., isNumber() returns NULL.

Returns
the value of this ASTNode as a string, or NULL if it is a node that does not have a name equivalent (e.g., if it is a number).

◆ getNumChildren()

unsigned int ASTNode::getNumChildren ( ) const

Returns the number of children of this node.

Returns
the number of children of this ASTNode, or 0 is this node has no children.
Examples
printMath.cpp.

◆ getNumerator()

long ASTNode::getNumerator ( ) const

Returns the value of the numerator of this node if of type AST_RATIONALendif.

◆ getNumSemanticsAnnotations()

unsigned int ASTNode::getNumSemanticsAnnotations ( ) const

Returns the number of MathML <semantics> element elements on this node.

The <semantics> element is a MathML 2.0 construct that can be used to associate additional information with a MathML construct. The construct can be used to decorate a MathML expressions with a sequence of one or more <annotation> or <annotation-xml> elements. Each such element contains a pair of items; the first is a symbol that acts as an attribute or key, and the second is the value associated with the attribute or key. Please refer to the MathML 2.0 documentation, particularly the Section 5.2, Semantic Annotations for more information about these constructs.
Returns
the number of annotations of this ASTNode.
Note
Although SBML permits the use of the MathML <semantics> annotation construct, the truth is that this construct has so far (at this time of this writing, which is early 2014) seen very little use in SBML software. The full implications of using these annotations are still poorly understood. If you wish to use this construct, we urge you to discuss possible uses and applications on the SBML discussion lists, particularly sbml-discuss and/or sbml-interoperability.
See also
addSemanticsAnnotation()
getSemanticsAnnotation()

◆ getOperatorName()

const char * ASTNode::getOperatorName ( ) const

Returns the value of this operator node as a string.

This function may be called on nodes that are operators, i.e., nodes for which isOperator() returns true.

Returns
the name of this operator ASTNode as a string (or NULL if not an operator).

◆ getParentSBMLObject()

SBase * ASTNode::getParentSBMLObject ( ) const

Returns the parent SBML object.

Returns
the parent SBML object of this ASTNode.
See also
isSetParentSBMLObject()
setParentSBMLObject()
unsetParentSBMLObject()

◆ getPrecedence()

int ASTNode::getPrecedence ( ) const

Returns the precedence of this node in the infix math syntax of SBML Level 1.

For more information about the infix syntax, see the discussion about text string formulas at the top of the documentation for ASTNode.

Returns
an integer indicating the precedence of this ASTNode

◆ getReal()

double ASTNode::getReal ( ) const

Returns the real-numbered value of this node.

This function performs the necessary arithmetic if the node type is AST_REAL_Eendif

◆ getRightChild()

ASTNode * ASTNode::getRightChild ( ) const

Returns the right child of this node.

Returns
the right child of this ASTNode, or NULL if this node has no right child. If getNumChildren() > 1, then this is equivalent to:
getChild( getNumChildren() - 1 );
See also
getNumChildren()
getLeftChild()
getChild()
Examples
createExampleSBML.cpp.

◆ getSemanticsAnnotation()

XMLNode * ASTNode::getSemanticsAnnotation ( unsigned int  n) const

Returns the nth MathML <semantics> element on this ASTNode.

The <semantics> element is a MathML 2.0 construct that can be used to associate additional information with a MathML construct. The construct can be used to decorate a MathML expressions with a sequence of one or more <annotation> or <annotation-xml> elements. Each such element contains a pair of items; the first is a symbol that acts as an attribute or key, and the second is the value associated with the attribute or key. Please refer to the MathML 2.0 documentation, particularly the Section 5.2, Semantic Annotations for more information about these constructs.
Parameters
nthe index of the annotation to return. Callers should use ASTNode::getNumSemanticsAnnotations() to first find out how many annotations there are.
Returns
the nth annotation inside this ASTNode, or NULL if this node has no nth annotation (n > getNumSemanticsAnnotations() - 1).
Note
Although SBML permits the use of the MathML <semantics> annotation construct, the truth is that this construct has so far (at this time of this writing, which is early 2014) seen very little use in SBML software. The full implications of using these annotations are still poorly understood. If you wish to use this construct, we urge you to discuss possible uses and applications on the SBML discussion lists, particularly sbml-discuss and/or sbml-interoperability.
See also
getNumSemanticsAnnotations()
addSemanticsAnnotation()

◆ getStyle()

std::string ASTNode::getStyle ( ) const

Returns the MathML style attribute value of this ASTNode.

Returns
the MathML style of this ASTNode, or an empty string if it does not exist.
See also
isSetStyle()
setStyle(const std::string& id)
unsetStyle()

◆ getType()

ASTNodeType_t ASTNode::getType ( ) const

Returns the type of this ASTNode.

The value returned is one of the Core AST type codes such as AST_LAMBDAendif

◆ getUnits()

std::string ASTNode::getUnits ( ) const

Returns the units of this ASTNode.

SBML Level 3 Version 1 introduced the ability to include an attribute sbml:units on MathML cn elements appearing in SBML mathematical formulas. The value of this attribute can be used to indicate the unit of measurement to be associated with the number in the content of the cn element. The value of this attribute must be the identifier of a unit of measurement defined by SBML or the enclosing Model. Here, the sbml portion is an XML namespace prefix that must be associated with the SBML namespace for SBML Level 3. The following example illustrates how this attribute can be used to define a number with value 10 and unit of measurement second:
<math xmlns="http://www.w3.org/1998/Math/MathML"
      xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
        <cn type="integer" sbml:units="second"> 10 </cn>
</math>
Returns
the units of this ASTNode.
Note
The sbml:units attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.
See also
SBML_parseL3Formula()

◆ getUserData()

void * ASTNode::getUserData ( ) const

Returns the user data that has been previously set via setUserData().

Returns
the user data of this node, or NULL if no user data has been set.
See also
isSetUserData()
setUserData()
unsetUserData()

◆ getValue()

double ASTNode::getValue ( ) const

Returns the numerical value of this ASTNode.

Returns
the numerical value of this ASTNode, or NaN if this is not a type of node that has a numerical value.
Note
This function will return a numerical value (as a double) for any ASTNode_t that represents a number, a constant such as AST_CONSTANT_PIendif

◆ hasCorrectNumberArguments()

bool ASTNode::hasCorrectNumberArguments ( ) const

Returns true if this ASTNode has the correct number of children for its type.

For example, an ASTNode with type AST_MINUSendif

◆ hasTypeAndNumChildren()

int ASTNode::hasTypeAndNumChildren ( ASTNodeType_t  type,
unsigned int  numchildren 
) const

Returns true if this node is of type type and has numchildren number of children.

Designed for use in cases where it is useful to discover if the node is a unary not or unary minus, or a times node with no children, etc.

Returns
true if this ASTNode is has the specified type and number of children, false otherwise.

◆ hasUnits()

bool ASTNode::hasUnits ( ) const

Returns true (nonzero) if this node or any of its children nodes have the attribute sbml:units.

SBML Level 3 Version 1 introduced the ability to include an attribute sbml:units on MathML cn elements appearing in SBML mathematical formulas. The value of this attribute can be used to indicate the unit of measurement to be associated with the number in the content of the cn element. The value of this attribute must be the identifier of a unit of measurement defined by SBML or the enclosing Model. Here, the sbml portion is an XML namespace prefix that must be associated with the SBML namespace for SBML Level 3. The following example illustrates how this attribute can be used to define a number with value 10 and unit of measurement second:
<math xmlns="http://www.w3.org/1998/Math/MathML"
      xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
        <cn type="integer" sbml:units="second"> 10 </cn>
</math>
Returns
true if this ASTNode or its children has units associated with it, false otherwise.
Note
The sbml:units attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.
See also
isSetUnits()
setUnits(const std::string& units)

◆ insertChild()

int ASTNode::insertChild ( unsigned int  n,
ASTNode disownedChild 
)

Inserts the given ASTNode at point n in the list of children of this ASTNode.

Parameters
nunsigned int the index of the ASTNode being added.
disownedChildASTNode to insert as the nth child.

◆ isAvogadro()

bool ASTNode::isAvogadro ( ) const

Returns true (nonzero) if this node is the special symbol avogadro.

The predicate returns false (zero) otherwise.

SBML Level 3 introduced a predefined MathML <csymbol> for the value of Avogadro's constant. LibSBML stores this internally as a node of type AST_NAME_AVOGADROendif

◆ isBoolean()

bool ASTNode::isBoolean ( ) const

Returns true if this node has a Boolean type.

The ASTNode objects that have Boolean types are the logical operators, relational operators, and the constants true or false.

Returns
true if this ASTNode has a Boolean type, false otherwise.

◆ isCiNumber()

bool ASTNode::isCiNumber ( ) const

Returns true (nonzero) if this node represents a MathML ci element representing a value not a function (e.g., true, Pi).

Returns
true if this ASTNode is a MathML ci element, false otherwise.

◆ isConstant()

bool ASTNode::isConstant ( ) const

Returns true (nonzero) if this node represents a MathML constant (e.g., true, Pi).

Returns
true if this ASTNode is a MathML constant, false otherwise.
Note
this function will also return true for nodes of type AST_NAME_AVOGADROendif

◆ isConstantNumber()

bool ASTNode::isConstantNumber ( ) const

Returns true (nonzero) if this node represents a MathML constant with numeric value (e.g., Pi).

Returns
true if this ASTNode is a MathML constant, false otherwise.
Note
this function will also return true for AST_NAME_AVOGADROendif

◆ isCSymbolFunction()

bool ASTNode::isCSymbolFunction ( ) const

Returns true (nonzero) if this node represents a MathML csymbol representing a function.

Returns
true if this ASTNode is a MathML csymbol function, false otherwise.

◆ isFunction()

bool ASTNode::isFunction ( ) const

Returns true if this node represents a function.

The three types of functions in SBML are MathML functions (e.g., abs()), SBML Level 1 functions (in the SBML Level 1 math syntax), and user-defined functions (using FunctionDefinition in SBML Level 2 and 3).

Returns
true if this ASTNode is a function, false otherwise.

◆ isInfinity()

bool ASTNode::isInfinity ( ) const

Returns true (nonzero) if this node represents the special IEEE 754 value infinity, false (zero) otherwise.

Returns
true if this ASTNode is the special IEEE 754 value infinity, false otherwise.

◆ isInteger()

bool ASTNode::isInteger ( ) const

Returns true (nonzero) if this node contains an integer value, false (zero) otherwise.

Returns
true if this ASTNode is of type AST_INTEGERendif

◆ isLambda()

bool ASTNode::isLambda ( ) const

Returns true (nonzero) if this node is a MathML <lambda>, false (zero) otherwise.

Returns
true if this ASTNode is of type AST_LAMBDAendif

◆ isLog10()

bool ASTNode::isLog10 ( ) const

Returns true (nonzero) if this node represents a log10 function, false (zero) otherwise.

More precisely, this predicate returns true if the node type is AST_FUNCTION_LOGendif

◆ isLogical()

bool ASTNode::isLogical ( ) const

Returns true (nonzero) if this node is a MathML logical operator.

The possible MathML logical operators in SBML core are and, or, not, xor, and (as of SBML Level 3 Version 2) implies. If the node represents a logical operator defined in a Level 3 package, it will also return true.

Returns
true if this ASTNode is a MathML logical operator, false otherwise.

◆ isName()

bool ASTNode::isName ( ) const

Returns true if this node is a user-defined variable name or the symbols for time or Avogadro's constant.

SBML Levels 2 and 3 provides <csymbol> definitions for "time" and "avogadro", which can be used to represent simulation time and Avogadro's constant in MathML. Note that this method does not return true for the other csymbol values defined by SBML, "delay", because the "delay" is a function and not a constant or variable. Similarly, this function returns false for the csymbol functions added by the 'Distributions' package.

Returns
true if this ASTNode is a user-defined variable name in SBML or the special symbols for time or Avogadro's constant. It returns false otherwise.

◆ isNaN()

bool ASTNode::isNaN ( ) const

Returns true (nonzero) if this node represents the special IEEE 754 value "not a number" (NaN), false (zero) otherwise.

Returns
true if this ASTNode is the special IEEE 754 NaN, false otherwise.

◆ isNegInfinity()

bool ASTNode::isNegInfinity ( ) const

Returns true (nonzero) if this node represents the special IEEE 754 value "negative infinity", false (zero) otherwise.

Returns
true if this ASTNode is the special IEEE 754 value negative infinity, false otherwise.

◆ isNumber()

bool ASTNode::isNumber ( ) const

Returns true (nonzero) if this node contains a number, false (zero) otherwise.

This is functionally equivalent to the following code:

isInteger() || isReal()
Returns
true if this ASTNode is a number, false otherwise.

◆ isOperator()

bool ASTNode::isOperator ( ) const

Returns true if this node is a mathematical operator.

The possible mathematical operators in the MathML syntax supported by SBML are +, -, *, / and ^ (power).

Returns
true if this ASTNode is an operator, false otherwise.

◆ isPiecewise()

bool ASTNode::isPiecewise ( ) const

Returns true (nonzero) if this node is the MathML <piecewise> construct.

Returns
true if this ASTNode is a MathML piecewise function, false (zero) otherwise.

◆ isRational()

bool ASTNode::isRational ( ) const

Returns true (nonzero) if this node represents a rational number.

Returns
true if this ASTNode is of type AST_RATIONALendif

◆ isReal()

bool ASTNode::isReal ( ) const

Returns true (nonzero) if this node can represent a real number, false (zero) otherwise.

More precisely, this node must be of one of the following types: AST_REALendif

◆ isRelational()

bool ASTNode::isRelational ( ) const

Returns true if this node is a MathML relational operator.

The MathML relational operators are ==, >=, >, <, and !=.

Returns
true if this ASTNode is a MathML relational operator, false otherwise

◆ isSetClass()

bool ASTNode::isSetClass ( ) const

Returns true (nonzero) if this node has a value for the MathML attribute "class".

Returns
true if this ASTNode has an attribute class, false otherwise.
See also
isSetId()
isSetStyle()
setClass()
unsetClass()

◆ isSetId()

bool ASTNode::isSetId ( ) const

Returns true (nonzero) if this node has a value for the MathML attribute "id".

Returns
true if this ASTNode has an attribute id, false otherwise.
See also
isSetClass()
isSetStyle()
setId(const std::string& id)
unsetId()

◆ isSetParentSBMLObject()

bool ASTNode::isSetParentSBMLObject ( ) const

Returns true if this node has a value for the parent SBML object.

Returns
true if this ASTNode has an parent SBML object set, false otherwise.
See also
getParentSBMLObject()
setParentSBMLObject()
unsetParentSBMLObject()

◆ isSetStyle()

bool ASTNode::isSetStyle ( ) const

Returns true (nonzero) if this node has a value for the MathML attribute "style".

Returns
true if this ASTNode has an attribute style, false otherwise.
See also
isSetClass()
isSetId()
setStyle(const std::string& id)
unsetStyle()

◆ isSetUnits()

bool ASTNode::isSetUnits ( ) const

Returns true (nonzero) if this node has the attribute sbml:units.

SBML Level 3 Version 1 introduced the ability to include an attribute sbml:units on MathML cn elements appearing in SBML mathematical formulas. The value of this attribute can be used to indicate the unit of measurement to be associated with the number in the content of the cn element. The value of this attribute must be the identifier of a unit of measurement defined by SBML or the enclosing Model. Here, the sbml portion is an XML namespace prefix that must be associated with the SBML namespace for SBML Level 3. The following example illustrates how this attribute can be used to define a number with value 10 and unit of measurement second:
<math xmlns="http://www.w3.org/1998/Math/MathML"
      xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
        <cn type="integer" sbml:units="second"> 10 </cn>
</math>
Returns
true if this ASTNode has units associated with it, false otherwise.
Note
The sbml:units attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.
See also
hasUnits()
setUnits(const std::string& units)

◆ isSetUserData()

bool ASTNode::isSetUserData ( ) const

Returns true if this node has a user data object.

Returns
true if this ASTNode has a user data object set, false otherwise.
See also
setUserData()
getUserData()
unsetUserData()

◆ isSqrt()

bool ASTNode::isSqrt ( ) const

Returns true (nonzero) if this node represents a square root function, false (zero) otherwise.

More precisely, the node type must be AST_FUNCTION_ROOTendif

◆ isUMinus()

bool ASTNode::isUMinus ( ) const

Returns true (nonzero) if this node is a unary minus operator, false (zero) otherwise.

A node is defined as a unary minus node if it is of type AST_MINUSendif

◆ isUnknown()

bool ASTNode::isUnknown ( ) const

Returns true (nonzero) if this node has an unknown type.

"Unknown" nodes have the type AST_UNKNOWNendif

◆ isUPlus()

bool ASTNode::isUPlus ( ) const

Returns true (nonzero) if this node is a unary plus operator, false (zero) otherwise.

A node is defined as a unary minus node if it is of type AST_MINUSendif

◆ isUserFunction()

bool ASTNode::isUserFunction ( ) const

Returns true (nonzero) if this node represents a MathML user-defined function.

Returns
true if this ASTNode is a user-defined function, false otherwise.

◆ isWellFormedASTNode()

bool ASTNode::isWellFormedASTNode ( ) const

Returns true or false depending on whether this ASTNode is well-formed.

Note
An ASTNode may be well-formed, with each node and its children having the appropriate number of children for the given type, but may still be invalid in the context of its use within an SBML model.
Returns
true if this ASTNode is well-formed, false otherwise.
See also
hasCorrectNumberArguments()

◆ operator=()

ASTNode & ASTNode::operator= ( const ASTNode rhs)

Assignment operator for ASTNode.

Parameters
rhsthe object whose values are used as the basis of the assignment.

◆ prependChild()

int ASTNode::prependChild ( ASTNode disownedChild)

Adds the given node as a child of this ASTNode.

This method adds child nodes from right to left.

Parameters
disownedChildthe ASTNode instance to add. Will become a child of the parent node.

◆ reduceToBinary()

void ASTNode::reduceToBinary ( )

Reduces this ASTNode to a binary tree.

Example: if this ASTNode is and(x, y, z), then the formula of the reduced node is and(and(x, y), z). The operation replaces the formula stored in the current ASTNode object.

◆ removeChild()

int ASTNode::removeChild ( unsigned int  n)

Removes the nth child of this ASTNode object.

Parameters
nunsigned int the index of the child to remove.

◆ renameSIdRefs()

void ASTNode::renameSIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtual

Renames all the SIdRef attributes on this node and any child node.

◆ renameUnitSIdRefs()

void ASTNode::renameUnitSIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtual

Renames all the UnitSIdRef attributes on this node and any child node.

The only place UnitSIDRefs appear is in MathML <cn> elements, so the effects of this method are limited to that.

Parameters
oldidthe old identifier.
newidthe new identifier.

◆ replaceArgument()

void ASTNode::replaceArgument ( const std::string &  bvar,
ASTNode arg 
)

Replaces occurrences of a given name with a given ASTNode.

For example, if the formula in this ASTNode is x + y, and the function is called with bvar = "x" and arg = an ASTNode representing the real value 3. This method would substitute 3 for x within this ASTNode object, resulting in the forula 3 + y.

Parameters
bvara string representing the variable name to be substituted.
argan ASTNode representing the name/value/formula to use as a replacement.

◆ replaceChild()

int ASTNode::replaceChild ( unsigned int  n,
ASTNode disownedChild,
bool  delreplaced = false 
)

Replaces and optionally deletes the nth child of this ASTNode with the given ASTNode.

Parameters
nunsigned int the index of the child to replace.
disownedChildASTNode to replace the nth child. Will become a child of the parent node.
delreplacedBoolean indicating whether to delete the replaced child.

◆ returnsBoolean()

bool ASTNode::returnsBoolean ( const Model model = NULL) const

Returns true (nonzero) if this node returns a Boolean type or false (zero) otherwise.

This function looks at the whole ASTNode rather than just the top level of the ASTNode. Thus it will consider return values from piecewise statements. In addition, if this ASTNode uses a function call, the return value of the functionDefinition will be determined. Note that this is only possible where the ASTNode can trace its parent Model, that is, the ASTNode must represent the <math> element of some SBML object that has already been added to an instance of an SBMLDocument. If this is not the case, this function will return false unless isBoolean() returns true.

See also
isBoolean()
Returns
true if this ASTNode returns a Boolean, false otherwise.

◆ setCharacter()

int ASTNode::setCharacter ( char  value)

Sets the value of this ASTNode to the given character.

If character is one of +, -, *, / or ^, the node type will be set accordingly. For all other characters, the node type will be set to AST_UNKNOWNendif

◆ setClass()

int ASTNode::setClass ( const std::string &  className)

Sets the MathML attribute class of this ASTNode to className.

Parameters
classNamestring representing the MathML class for this node.

◆ setId()

int ASTNode::setId ( const std::string &  id)

Sets the MathML attribute id of this ASTNode.

Parameters
idstring representing the identifier.

◆ setName()

int ASTNode::setName ( const char *  name)

Sets the value of this ASTNode to the given name.

As a side effect, this ASTNode object's type will be reset to AST_NAMEendif

Examples
createExampleSBML.cpp.

◆ setStyle()

int ASTNode::setStyle ( const std::string &  style)

Sets the MathML attribute style of this ASTNode to style.

Parameters
stylestring representing the identifier.

◆ setType()

int ASTNode::setType ( ASTNodeType_t  type)

Sets the type of this ASTNode to the given type code.

Parameters
typethe type to which this node should be set.

◆ setUnits()

int ASTNode::setUnits ( const std::string &  units)

Sets the units of this ASTNode to units.

The units will be set only if this ASTNode object represents a MathML <cn> element, i.e., represents a number. Callers may use isNumber() to inquire whether the node is of that type.

SBML Level 3 Version 1 introduced the ability to include an attribute sbml:units on MathML cn elements appearing in SBML mathematical formulas. The value of this attribute can be used to indicate the unit of measurement to be associated with the number in the content of the cn element. The value of this attribute must be the identifier of a unit of measurement defined by SBML or the enclosing Model. Here, the sbml portion is an XML namespace prefix that must be associated with the SBML namespace for SBML Level 3. The following example illustrates how this attribute can be used to define a number with value 10 and unit of measurement second:
<math xmlns="http://www.w3.org/1998/Math/MathML"
      xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
        <cn type="integer" sbml:units="second"> 10 </cn>
</math>
Parameters
unitsstring representing the unit identifier.

◆ setUserData()

int ASTNode::setUserData ( void *  userData)

Sets the user data of this node.

The user data can be used by the application developer to attach custom information to the node. In case of a deep copy, this attribute will passed as it is. The attribute will be never interpreted by this class.

Parameters
userDataspecifies the new user data.

◆ setValue() [1/5]

int ASTNode::setValue ( double  mantissa,
long  exponent 
)

Sets the value of this ASTNode to the given real (double) in two parts: the mantissa and the exponent.

The node type is set to AST_REAL_Eendif

◆ setValue() [2/5]

int ASTNode::setValue ( double  value)

Sets the value of this ASTNode to the given real (double) and sets the node type to AST_REALendif.

◆ setValue() [3/5]

int ASTNode::setValue ( int  value)

Sets the value of this ASTNode to the given integer and sets the node type to AST_INTEGERendif.

◆ setValue() [4/5]

int ASTNode::setValue ( long  numerator,
long  denominator 
)

Sets the value of this ASTNode to the given rational in two parts: the numerator and denominator.

The node type is set to AST_RATIONALendif

◆ setValue() [5/5]

int ASTNode::setValue ( long  value)

Sets the value of this ASTNode to the given (long) integer and sets the node type to AST_INTEGERendif.

◆ swapChildren()

int ASTNode::swapChildren ( ASTNode that)

Swaps the children of this ASTNode object with the children of the given ASTNode object.

Parameters
thatthe other node whose children should be used to replace this node's children.

◆ unsetClass()

int ASTNode::unsetClass ( )

Unsets the MathML class attribute of this ASTNode.

◆ unsetId()

int ASTNode::unsetId ( )

Unsets the MathML id attribute of this ASTNode.

◆ unsetParentSBMLObject()

int ASTNode::unsetParentSBMLObject ( )

Unsets the parent SBML object.

◆ unsetStyle()

int ASTNode::unsetStyle ( )

Unsets the MathML style attribute of this ASTNode.

◆ unsetUnits()

int ASTNode::unsetUnits ( )

Unsets the units of this ASTNode.

◆ unsetUserData()

int ASTNode::unsetUserData ( )

Unsets the user data of this node.

The user data can be used by the application developer to attach custom information to the node. In case of a deep copy, this attribute will passed as it is. The attribute will be never interpreted by this class.