libSBML Perl API  libSBML 5.15.2 Perl API
ASTNode Class Reference
Inheritance diagram for ASTNode:
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Detailed Description

{core}

Abstract Syntax Trees for mathematical expressions.

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. 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).

The set of possible ASTNode types

Converting between ASTs and text strings

The text-string form of mathematical formulas produced by

Public Member Functions

int addChild (ASTNode *disownedChild)
 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)
 Creates a new ASTNode. More...
 
 ASTNode (Token_t *token)
 Creates a new ASTNode from the given Token. More...
 
 ASTNode (const ASTNode &orig)
 Copy constructor; creates a deep copy of the given ASTNode. More...
 
bool canonicalize ()
 Converts this ASTNode to a canonical form. 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...
 
char getCharacter () const
 Returns the value of this node as a single character. More...
 
virtual 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...
 
virtual int getExtendedType () const
 Returns the extended type 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. 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 (int type, unsigned int numchildren) const
 Returns true if this node is of a certain type with a specific number of children. More...
 
bool hasUnits () const
 Returns true 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 node at a given point in the current ASTNode's list of children. More...
 
virtual bool isAvogadro () const
 Returns true if this node represents the predefined value for Avogadro's constant. More...
 
virtual bool isBoolean () const
 Returns true if this node has a Boolean type. More...
 
virtual bool isConstant () const
 Returns true if this node represents a MathML constant. More...
 
virtual bool isConstantNumber () const
 Returns true if this node represents a MathML constant numeric. More...
 
virtual bool isFunction () const
 Returns true if this node represents a function. More...
 
bool isInfinity () const
 Returns true if this node represents the special IEEE 754 value for infinity. More...
 
virtual bool isInteger () const
 Returns true if this node of type. More...
 
virtual bool isLambda () const
 Returns true if this node is a MathML <lambda>. More...
 
virtual bool isLog10 () const
 Returns true if this node represents a log10 function. More...
 
virtual bool isLogical () const
 Returns true if this node is a MathML logical operator. More...
 
virtual 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 if this node represents the special IEEE 754 value "not a number" (NaN). More...
 
bool isNegInfinity () const
 Returns true if this node represents the special IEEE 754 value "negative infinity". More...
 
virtual bool isNumber () const
 Returns true if this node contains a number. More...
 
virtual bool isOperator () const
 Returns true if this node is a mathematical operator. More...
 
virtual bool isPiecewise () const
 Returns true if this node is the MathML <piecewise> construct. More...
 
virtual bool isQualifier () const
 Predicate returning true if this node is a MathML qualifier. More...
 
virtual bool isRational () const
 Returns true if this node represents a rational number. More...
 
virtual bool isReal () const
 Returns true if this node can represent a real number. More...
 
virtual bool isRelational () const
 Returns true if this node is a MathML relational operator. More...
 
virtual bool isSemantics () const
 Predicate returning true if this node is a MathML semantics node. More...
 
bool isSetClass () const
 Returns true if this node has a value for the MathML attribute class. More...
 
bool isSetId () const
 Returns true 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 if this node has a value for the MathML attribute style. More...
 
bool isSetUnits () const
 Returns true 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 if this node represents a square root function. More...
 
bool isUMinus () const
 Returns true if this node is a unary minus operator. More...
 
virtual bool isUnknown () const
 Returns true if this node has an unknown type. More...
 
bool isUPlus () const
 Returns true if this node is a unary plus operator. 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 its child nodes. More...
 
virtual void renameUnitSIdRefs (const std::string &oldid, const std::string &newid)
 Renames all the UnitSIdRef attributes on this node and its child nodes. 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 the nth child of this ASTNode with the given ASTNode. More...
 
bool returnsBoolean (const Model *model=NULL) const
 Returns true if this node returns a Boolean value. 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. More...
 
int setDefinitionURL (XMLAttributes url)
 Sets the MathML attribute definitionURL. More...
 
int setDefinitionURL (const std::string &url)
 Sets the MathML attribute definitionURL. 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 setParentSBMLObject (SBase *sb)
 Sets the parent SBML object of this node. More...
 
int setStyle (const std::string &style)
 Sets the MathML attribute style of this ASTNode. More...
 
int setType (ASTNodeType_t type)
 Sets the type of this ASTNode to the given type code. More...
 
int setType (int type)
 Sets the type of this ASTNode. 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 (int value)
 Sets the value of this ASTNode to the given integer. More...
 
int setValue (long value)
 Sets the value of this ASTNode to the given (long) integer. More...
 
int setValue (long numerator, long denominator)
 Sets the value of this ASTNode to the given rational. More...
 
int setValue (double value)
 Sets the value of this ASTNode to the given real (double). More...
 
int setValue (double mantissa, long exponent)
 Sets the value of this ASTNode to the given real (double) More...
 
int swapChildren (ASTNode *that)
 Swaps the children of this node with the children of another node. 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...
 

Friends

class ASTSemanticsNode
 

Constructor & Destructor Documentation

◆ ASTNode() [1/3]

ASTNode::ASTNode ( ASTNodeType_t  type)

Creates a new ASTNode.

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

◆ 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 given 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)

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. Will become a child of the parent node.

◆ addSemanticsAnnotation()

int ASTNode::addSemanticsAnnotation ( XMLNode disownedAnnotation)

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

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.

The rules determining the canonical form conversion are as follows:

  • If the node type is

◆ 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 ASTNode::getListOfNodes(), 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.

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

◆ getCharacter()

char ASTNode::getCharacter ( ) const

Returns the value of this node as a single character.

This function should be called only when ASTNode::getType() returns

◆ getChild()

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

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 > ASTNode::getNumChildren() - 1).
See also
getNumChildren()
getLeftChild()
getRightChild()

◆ getClass()

std::string ASTNode::getClass ( ) const

Returns the MathML class attribute value of this ASTNode.

Returns
the MathML class of this ASTNode, if any exists.
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 if this node is not of type

◆ 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 ASTNode::getType() returns

◆ getExtendedType()

int ASTNode::getExtendedType ( ) const
virtual

Returns the extended type of this ASTNode.

The type may be either a core integer type codeor a value of a type code defined by an SBML Level 3 package.

Returns
the type of this ASTNode.
Note
When the ASTNode is of a type from a package, the value returned by ASTNode::getType() will be

◆ 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

◆ getLeftChild()

ASTNode * ASTNode::getLeftChild ( ) const

Returns the left child of this node.

Returns
the left child of this ASTNode. This is equivalent to calling ASTNode::getChild(unsigned int) with an argument of 0.
See also
getNumChildren()
getChild()
getRightChild()

◆ 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. For portability between different programming languages, the predicate is passed in as a pointer to a function.

Parameters
predicatethe predicate to use.
Returns
the list of nodes for which the predicate returned true. 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.
See also
fillListOfNodes()

◆ getMantissa()

double ASTNode::getMantissa ( ) const

Returns the mantissa value of this node.

If ASTNode::getType() returns

◆ 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 ASTNode::isOperator() returns false, and (2) are not numbers, i.e., ASTNode::isNumber() returns false.

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.

◆ getNumerator()

long ASTNode::getNumerator ( ) const

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

◆ getNumSemanticsAnnotations()

unsigned int ASTNode::getNumSemanticsAnnotations ( ) const

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

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 ASTNode::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()
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

◆ 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 ASTNode::getNumChildren() > 1, then this is equivalent to:
getChild( getNumChildren() - 1 );
See also
getNumChildren()
getLeftChild()
getChild()

◆ getSemanticsAnnotation()

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

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

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 > ASTNode::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
addSemanticsAnnotation()
getNumSemanticsAnnotations()

◆ getStyle()

std::string ASTNode::getStyle ( ) const

Returns the MathML style attribute value of this ASTNode.

Returns
the MathML style of this ASTNode, if any exists.
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

◆ 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

◆ 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.

◆ 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

◆ 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

◆ hasTypeAndNumChildren()

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

Returns true if this node is of a certain type with a specific 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.

Parameters
typethe type of ASTNode sought.
numchildrenthe number of child nodes sought.
Returns
true if this ASTNode is has the specified type and number of children, false otherwise.

◆ hasUnits()

bool ASTNode::hasUnits ( ) const

Returns true 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 node at a given point in the current ASTNode's list of children.

Parameters
nunsigned int the index of the ASTNode being added.
disownedChildASTNode to insert as the nth child. Will become a child of the parent node.

◆ isAvogadro()

bool ASTNode::isAvogadro ( ) const
virtual

Returns true if this node represents the predefined value for Avogadro's constant.

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

◆ isBoolean()

bool ASTNode::isBoolean ( ) const
virtual

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.

◆ isConstant()

bool ASTNode::isConstant ( ) const
virtual

Returns true if this node represents a MathML constant.

Examples of MathML constants include such things as pi.

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

◆ isConstantNumber()

bool ASTNode::isConstantNumber ( ) const
virtual

Returns true if this node represents a MathML constant numeric.

Examples of MathML constants include such things as pi.

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

◆ isFunction()

bool ASTNode::isFunction ( ) const
virtual

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 if this node represents the special IEEE 754 value for infinity.

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

◆ isInteger()

bool ASTNode::isInteger ( ) const
virtual

Returns true if this node of type.

◆ isLambda()

bool ASTNode::isLambda ( ) const
virtual

Returns true if this node is a MathML <lambda>.

Returns
true if this ASTNode is of type

◆ isLog10()

bool ASTNode::isLog10 ( ) const
virtual

Returns true if this node represents a log10 function.

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

◆ isLogical()

bool ASTNode::isLogical ( ) const
virtual

Returns true 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
virtual

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.

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 if this node represents the special IEEE 754 value "not a number" (NaN).

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

◆ isNegInfinity()

bool ASTNode::isNegInfinity ( ) const

Returns true if this node represents the special IEEE 754 value "negative infinity".

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

◆ isNumber()

bool ASTNode::isNumber ( ) const
virtual

Returns true if this node contains a number.

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

◆ isOperator()

bool ASTNode::isOperator ( ) const
virtual

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
virtual

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

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

◆ isQualifier()

bool ASTNode::isQualifier ( ) const
virtual

Predicate returning true if this node is a MathML qualifier.

The MathML qualifier node types are bvar, degree, base, piece, and otherwise.

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

◆ isRational()

bool ASTNode::isRational ( ) const
virtual

Returns true if this node represents a rational number.

Returns
true if this ASTNode is of type

◆ isReal()

bool ASTNode::isReal ( ) const
virtual

Returns true if this node can represent a real number.

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

◆ isRelational()

bool ASTNode::isRelational ( ) const
virtual

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.

◆ isSemantics()

bool ASTNode::isSemantics ( ) const
virtual

Predicate returning true if this node is a MathML semantics node.

Returns
true if this ASTNode is a MathML semantics node, false otherwise.

◆ isSetClass()

bool ASTNode::isSetClass ( ) const

Returns true 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 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()
unsetParentSBMLObject()

◆ isSetStyle()

bool ASTNode::isSetStyle ( ) const

Returns true 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 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.

◆ isSqrt()

bool ASTNode::isSqrt ( ) const

Returns true if this node represents a square root function.

More precisely, the node type must be

◆ isUMinus()

bool ASTNode::isUMinus ( ) const

Returns true if this node is a unary minus operator.

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

◆ isUnknown()

bool ASTNode::isUnknown ( ) const
virtual

Returns true if this node has an unknown type.

"Unknown" nodes have the type

◆ isUPlus()

bool ASTNode::isUPlus ( ) const

Returns true if this node is a unary plus operator.

A node is defined as a unary plus node if it is of type

◆ 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 its child nodes.

Parameters
oldidthe old identifier.
newidthe new identifier.

◆ renameUnitSIdRefs()

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

Renames all the UnitSIdRef attributes on this node and its child nodes.

The only place UnitSIDRefs appear 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 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 if this node returns a Boolean value.

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 to a user-defined function, the return value of the corresponding FunctionDefinition object 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.

Parameters
modelthe Model to use as context.
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

◆ setClass()

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

Sets the MathML attribute class of this ASTNode.

Parameters
classNamestring representing the MathML class for this node.

◆ setDefinitionURL() [1/2]

int ASTNode::setDefinitionURL ( XMLAttributes  url)

Sets the MathML attribute definitionURL.

Parameters
urlthe URL value for the definitionURL attribute.

◆ setDefinitionURL() [2/2]

int ASTNode::setDefinitionURL ( const std::string &  url)

Sets the MathML attribute definitionURL.

Parameters
urlthe URL value for the definitionURL attribute.

◆ 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

◆ setParentSBMLObject()

int ASTNode::setParentSBMLObject ( SBase sb)

Sets the parent SBML object of this node.

Is not recursive, and will not set the parent SBML object of any children of this node.

Parameters
sbthe parent SBML object of this ASTNode.

◆ setStyle()

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

Sets the MathML attribute style of this ASTNode.

Parameters
stylestring representing the identifier.

◆ setType() [1/2]

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.

◆ setType() [2/2]

int ASTNode::setType ( int  type)

Sets the type of this ASTNode.

This uses integer type codes, which may come from the set of static integer constants whose names begin with the prefix AST_ or an enumeration of AST types in an SBML Level 3 package.

Parameters
typethe integer representing the 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 ASTNode::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 ( int  value)

Sets the value of this ASTNode to the given integer.

As a side effect, this operation sets the node type to

◆ setValue() [2/5]

int ASTNode::setValue ( long  value)

Sets the value of this ASTNode to the given (long) integer.

As a side effect, this operation sets the node type to

◆ setValue() [3/5]

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

Sets the value of this ASTNode to the given rational.

As a side effect, this operation sets the node type to

◆ setValue() [4/5]

int ASTNode::setValue ( double  value)

Sets the value of this ASTNode to the given real (double).

As a side effect, this operation sets the node type to

◆ setValue() [5/5]

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

Sets the value of this ASTNode to the given real (double)

As a side effet, this operation sets the node type to

◆ swapChildren()

int ASTNode::swapChildren ( ASTNode that)

Swaps the children of this node with the children of another node.

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.

Friends And Related Function Documentation

◆ ASTSemanticsNode

friend class ASTSemanticsNode
friend