Detailed Description

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).

: An AST node in libSBML is a recursive tree structure; each node has a type, a pointer to a value, and a list of children nodes. Each ASTNode node may have none, one, two, or more children depending on its type. 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. The following diagram illustrates an example of how the mathematical expression "1 + 2" is represented as an AST with one plus node having two integer children nodes for the numbers 1 and 2. The figure also shows the corresponding MathML representation:

Example AST representation of a mathematical expression.
Infix	AST	MathML
`1 + 2`		`<math xmlns="http://www.w3.org/1998/Math/MathML">` `<apply>` `<plus/>` `<cn type="integer"> 1 </cn>` `<cn type="integer"> 2 </cn>` `</apply>` `</math>`

The following are other noteworthy points about the AST representation in libSBML:

A numerical value represented in MathML as a real number with an exponent is preserved as such in the AST node representation, even if the number could be stored in a double data type. This is done so that when an SBML model is read in and then written out again, the amount of change introduced by libSBML to the SBML during the round-trip activity is minimized.

Rational numbers are represented in an AST node using separate numerator and denominator values. These can be retrieved using the methods ASTNode::getNumerator() and ASTNode::getDenominator().

The children of an ASTNode are other ASTNode objects. The list of children is empty for nodes that are leaf elements, such as numbers. For nodes that are actually roots of expression subtrees, the list of children points to the parsed objects that make up the rest of the expression.

For many applications, the details of ASTs are irrelevant because libSBML provides text-string based translation functions such as SBML_formulaToL3String() and SBML_parseL3Formula(). If you find the complexity of using the AST representation of expressions too high for your purposes, perhaps the string-based functions will be more suitable.

ASTNodeType_t

: Every ASTNode has an associated type code to indicate whether, for example, it holds a number or stands for an arithmetic operator. The type is recorded as a value drawn from the enumeration ASTNodeType_t. The list of possible types is quite long, because it covers all the mathematical functions that are permitted in SBML. The values are shown in the following table:

AST_CONSTANT_E	AST_FUNCTION_CSC	AST_LOGICAL_AND
AST_CONSTANT_FALSE	AST_FUNCTION_CSCH	AST_LOGICAL_IMPLIES²
AST_CONSTANT_PI	AST_FUNCTION_DELAY	AST_LOGICAL_NOT
AST_CONSTANT_TRUE	AST_FUNCTION_EXP	AST_LOGICAL_OR
AST_DIVIDE	AST_FUNCTION_FACTORIAL	AST_LOGICAL_XOR
AST_FUNCTION	AST_FUNCTION_FLOOR	AST_MINUS
AST_FUNCTION_ABS	AST_FUNCTION_LN	AST_NAME
AST_FUNCTION_ARCCOS	AST_FUNCTION_LOG	AST_NAME_AVOGADRO¹
AST_FUNCTION_ARCCOSH	AST_FUNCTION_MAX²	AST_NAME_TIME
AST_FUNCTION_ARCCOT	AST_FUNCTION_MIN²	AST_ORIGINATES_IN_PACKAGE²
AST_FUNCTION_ARCCOTH	AST_FUNCTION_PIECEWISE	AST_PLUS
AST_FUNCTION_ARCCSC	AST_FUNCTION_POWER	AST_POWER
AST_FUNCTION_ARCCSCH	AST_FUNCTION_QUOTIENT²	AST_RATIONAL
AST_FUNCTION_ARCSEC	AST_FUNCTION_RATE_OF²	AST_REAL
AST_FUNCTION_ARCSECH	AST_FUNCTION_REM²	AST_REAL_E
AST_FUNCTION_ARCSIN	AST_FUNCTION_ROOT	AST_RELATIONAL_EQ
AST_FUNCTION_ARCSINH	AST_FUNCTION_SEC	AST_RELATIONAL_GEQ
AST_FUNCTION_ARCTAN	AST_FUNCTION_SECH	AST_RELATIONAL_GT
AST_FUNCTION_ARCTANH	AST_FUNCTION_SIN	AST_RELATIONAL_LEQ
AST_FUNCTION_CEILING	AST_FUNCTION_SINH	AST_RELATIONAL_LT
AST_FUNCTION_COS	AST_FUNCTION_TAN	AST_RELATIONAL_NEQ
AST_FUNCTION_COSH	AST_FUNCTION_TANH	AST_TIMES
AST_FUNCTION_COT	AST_INTEGER	AST_UNKNOWN
AST_FUNCTION_COTH	AST_LAMBDA
¹ (Level 3 only)
² (Level 3 Version 2+ only)

The types have the following meanings:

If the node is basic mathematical operator (e.g., "+"), then the node's type will be AST_PLUS, AST_MINUS, AST_TIMES, AST_DIVIDE, or AST_POWER, as appropriate.

If the node is a predefined function or operator from SBML Level 1 (in the string-based formula syntax used in Level 1) or SBML Level 2 and 3 (in the subset of MathML used in SBML Levels 2 and 3), then the node's type will be either AST_FUNCTION_X, AST_LOGICAL_X, or AST_RELATIONAL_X, as appropriate. (Examples: AST_FUNCTION_LOG, AST_RELATIONAL_LEQ.)

If the node refers to a user-defined function, the node's type will be AST_FUNCTION (because it holds the name of the function).

If the node is a lambda expression, its type will be AST_LAMBDA.

If the node is a predefined constant ("ExponentialE", "Pi", "True" or "False"), then the node's type will be AST_CONSTANT_E, AST_CONSTANT_PI, AST_CONSTANT_TRUE, or AST_CONSTANT_FALSE.

(Levels 2 and 3 only) If the node is the special MathML csymbol time, the value of the node will be AST_NAME_TIME. (Note, however, that the MathML csymbol delay is translated into a node of type AST_FUNCTION_DELAY. The difference is due to the fact that time is a single variable, whereas delay is actually a function taking arguments.)

(Level 3 only) If the node is the special MathML csymbol avogadro, the value of the node will be AST_NAME_AVOGADRO.

(Level 3 Version 2+ only) If the node is the special MathML csymbol rateOf, the value of the node will be AST_FUNCTION_RATE_OF.

(Level 3 Version 2+ only) If the node is a MathML operator that originates in a package, it is included in the ASTNodeType_t list, but may not be legally used in an SBML document that does not include that package. This includes the node types from the 'Distributions' package (AST_DISTRIB_FUNCTION_NORMAL, AST_DISTRIB_FUNCTION_UNIFORM, etc.), and elements from MathML that were not included in core.

If the node contains a numerical value, its type will be AST_INTEGER, AST_REAL, AST_REAL_E, or AST_RATIONAL, as appropriate.

Converting between ASTs and text strings

The text-string form of mathematical formulas produced by SBML_formulaToString() and read by SBML_parseFormula() and SBML_parseL3Formula() are in a simple C-inspired infix notation. A formula in this text-string form can be handed to a program that understands SBML mathematical expressions, or used as part of a translation system. The libSBML distribution comes with an example program in the "examples" subdirectory called translateMath that implements an interactive command-line demonstration of translating infix formulas into MathML and vice-versa.

The formula strings may contain operators, function calls, symbols, and white space characters. The allowable white space characters are tab and space. The following are illustrative examples of formulas expressed in the syntax:

0.10 * k4^2

(vm * s1)/(km + s1)

The following table shows the precedence rules in this syntax. In the Class column, operand implies the construct is an operand, prefix implies the operation is applied to the following arguments, unary implies there is one argument, and binary implies there are two arguments. The values in the Precedence column show how the order of different types of operation are determined. For example, the expression a * b + c is evaluated as (a * b) + c because the * operator has higher precedence. The Associates column shows how the order of similar precedence operations is determined; for example, a - b + c is evaluated as (a - b) + c because the + and - operators are left-associative. The precedence and associativity rules are taken from the C programming language, except for the symbol ^, which is used in C for a different purpose. (Exponentiation can be invoked using either ^ or the function power.)

A table of the expression operators and their precedence in the text-string format for mathematical expressions used by SBML_parseFormula().
Token	Operation	Class	Precedence	Associates
name	symbol reference	operand	6	n/a
`(`expression`)`	expression grouping	operand	6	n/a
`f(`...`)`	function call	prefix	6	left
`-`	negation	unary	5	right
`^`	power	binary	4	left
`*`	multiplication	binary	3	left
`/`	divison	binary	3	left
`+`	addition	binary	2	left
`-`	subtraction	binary	2	left
`,`	argument delimiter	binary	1	left

A program parsing a formula in an SBML model should assume that names appearing in the formula are the identifiers of Species, Parameter, Compartment, FunctionDefinition, Reaction (in SBML Levels 2 and 3), or SpeciesReference (in SBML Level 3 only) objects defined in a model. When a function call is involved, the syntax consists of a function identifier, followed by optional white space, followed by an opening parenthesis, followed by a sequence of zero or more arguments separated by commas (with each comma optionally preceded and/or followed by zero or more white space characters), followed by a closing parenthesis. There is an almost one-to-one mapping between the list of predefined functions available, and those defined in MathML. All of the MathML functions are recognized; this set is larger than the functions defined in SBML Level 1. In the subset of functions that overlap between MathML and SBML Level 1, there exist a few differences. The following table summarizes the differences between the predefined functions in SBML Level 1 and the MathML equivalents in SBML Levels 2 and 3:

Table comparing the names of certain functions in the SBML text-string formula syntax and MathML. The left column shows the names of functions recognized by SBML_parseFormula(); the right column shows their equivalent function names in MathML 2.0, used in SBML Levels 2 and 3.
Text string formula functions	MathML equivalents in SBML Levels 2 and 3
`acos`	`arccos`
`asin`	`arcsin`
`atan`	`arctan`
`ceil`	`ceiling`
`log`	`ln`
`log10(x)`	`log(x)` or `log(10, x)`
`pow(x, y)`	`power(x, y)`
`sqr(x)`	`power(x, 2)`
`sqrt(x)`	`root(x)` or `root(2, x)`

See also: SBML_parseL3Formula(); SBML_parseFormula()

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 semantic annotation of this ASTNode. More...

	ASTNode (ASTNodeType_t type=AST_UNKNOWN)
	Creates and returns 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 and returns `true` if successful, `false` otherwise. More...

ASTNode *	deepCopy () 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 (const SBMLNamespaces *sbmlns)

ASTBasePlugin *	getASTPlugin (ASTNodeType_t type)

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

const ASTBasePlugin *	getASTPlugin (const SBMLNamespaces *sbmlns) const

const ASTBasePlugin *	getASTPlugin (ASTNodeType_t type) const

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

char	getCharacter () const
	Gets the value of this node as a single character. More...

ASTNode *	getChild (unsigned int n) const
	Gets a child of this node according to its index number. More...

std::string	getClass () const
	Gets the class of this ASTNode. More...

XMLAttributes *	getDefinitionURL () const
	Gets the MathML "definitionURL" attribute value. More...

std::string	getDefinitionURLString () const
	Returns the MathML `definitionURL` attribute value as a string. More...

long	getDenominator () const
	Gets the value of the denominator of this node. More...

long	getExponent () const
	Gets the exponent value of this ASTNode. More...

std::string	getId () const
	Gets the id of this ASTNode. More...

long	getInteger () const
	Gets the value of this node as an integer. More...

ASTNode *	getLeftChild () const
	Gets the left child of this node. More...

List *	getListOfNodes (ASTNodePredicate predicate) const
	Returns a list of nodes satisfying a given predicate. More...

double	getMantissa () const
	Gets the mantissa value of this node. More...

const char *	getName () const
	Gets the value of this node as a string. More...

unsigned int	getNumChildren () const
	Gets the number of children that this node has. More...

long	getNumerator () const
	Gets the value of the numerator of this node. More...

unsigned int	getNumSemanticsAnnotations () const
	Gets the number of semantic annotation elements inside this node. More...

const char *	getOperatorName () const
	Gets the value of this operator node as a string. More...

SBase *	getParentSBMLObject () const
	Returns the parent SBML object. More...

int	getPrecedence () const
	Gets the precedence of this node in the infix math syntax of SBML Level 1. More...

double	getReal () const
	Gets the real-numbered value of this node. More...

ASTNode *	getRightChild () const
	Gets the right child of this node. More...

XMLNode *	getSemanticsAnnotation (unsigned int n) const
	Gets the nth semantic annotation of this node. More...

std::string	getStyle () const
	Gets the style of this ASTNode. More...

ASTNodeType_t	getType () const
	Gets the type of this ASTNode. More...

std::string	getUnits () const
	Gets 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` or `false` depending on whether 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. More...

bool	hasUnits () const
	Returns `true` (non-zero) 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` (non-zero) if this node is the special symbol `avogadro`. More...

bool	isBoolean () const
	Returns `true` (non-zero) if this node has a boolean type (a logical operator, a relational operator, or the constants `true` or `false`). More...

bool	isCiNumber () const
	Returns `true` (non-zero) if this node represents a MathML ci element representing a value not a function (e.g., `true`, `Pi`). More...

bool	isConstant () const
	Returns `true` (non-zero) if this node represents a MathML constant (e.g., `true`, `Pi`). More...

bool	isConstantNumber () const
	Returns `true` (non-zero) if this node represents a MathML constant with numeric value(e.g., `Pi`). More...

bool	isCSymbolFunction () const
	Returns `true` (non-zero) if this node represents a MathML csymbol representing a function. More...

bool	isFunction () const
	Returns `true` (non-zero) if this node represents a MathML function (e.g., `abs()`), or an SBML Level 1 function, or a user-defined function. More...

bool	isInfinity () const
	Returns `true` (non-zero) if this node represents the special IEEE 754 value infinity, `false` (zero) otherwise. More...

bool	isInteger () const
	Returns `true` (non-zero) if this node contains an integer value, `false` (zero) otherwise. More...

bool	isLambda () const
	Returns `true` (non-zero) if this node is a MathML `<lambda>`, `false` (zero) otherwise. More...

bool	isLog10 () const
	Returns `true` (non-zero) if this node represents a `log10` function, `false` (zero) otherwise. More...

bool	isLogical () const
	Returns `true` (non-zero) if this node is a MathML logical operator (i.e., `and`, `or`, `not`, `xor`). More...

bool	isName () const
	Returns `true` (non-zero) if this node is a user-defined variable name in SBML L1, L2 (MathML), or the special symbols `time` or `avogadro`. More...

bool	isNaN () const
	Returns `true` (non-zero) if this node represents the special IEEE 754 value "not a number" (NaN), `false` (zero) otherwise. More...

bool	isNegInfinity () const
	Returns `true` (non-zero) if this node represents the special IEEE 754 value "negative infinity", `false` (zero) otherwise. More...

bool	isNumber () const
	Returns `true` (non-zero) if this node contains a number, `false` (zero) otherwise. More...

bool	isOperator () const
	Returns `true` (non-zero) if this node is a mathematical operator, meaning, `+`, `-`, `*`, `/` or `^` (power). More...

bool	isPiecewise () const
	Returns `true` (non-zero) if this node is the MathML `<piecewise>` construct, `false` (zero) otherwise. More...

bool	isRational () const
	Returns `true` (non-zero) if this node represents a rational number, `false` (zero) otherwise. More...

bool	isReal () const
	Returns `true` (non-zero) if this node can represent a real number, `false` (zero) otherwise. More...

bool	isRelational () const
	Returns `true` (non-zero) if this node is a MathML relational operator, meaning `==`, `>=`, `>`, `<`, and `!=`. More...

bool	isSetClass () const
	Returns `true` (non-zero) if this node has a value for the MathML attribute "class". More...

bool	isSetId () const
	Returns `true` (non-zero) 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` (non-zero) if this node has a value for the MathML attribute "style". More...

bool	isSetUnits () const
	Returns `true` (non-zero) 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` (non-zero) if this node represents a square root function, `false` (zero) otherwise. More...

bool	isUMinus () const
	Returns `true` (non-zero) if this node is a unary minus operator, `false` (zero) otherwise. More...

bool	isUnknown () const
	Returns `true` (non-zero) if this node has an unknown type. More...

bool	isUPlus () const
	Returns `true` (non-zero) if this node is a unary plus operator, `false` (zero) otherwise. More...

bool	isUserFunction () const
	Returns `true` (non-zero) 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...

ASTNode &	operator= (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 occurences of a given name within this ASTNode with the name/value/formula represented by `arg`. 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` (non-zero) 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 class of this ASTNode to className. More...

int	setId (const std::string &id)
	Sets the MathML id of this ASTNode to id. 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 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 (int value)
	Sets the value of this ASTNode to the given integer and sets the node type to AST_INTEGER. More...

int	setValue (long value)
	Sets the value of this ASTNode to the given (`long`) integer and sets the node type to AST_INTEGER. 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 (double value)
	Sets the value of this ASTNode to the given real (`double`) and sets the node type to AST_REAL. 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	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 of this ASTNode. More...

int	unsetId ()
	Unsets the MathML id of this ASTNode. More...

int	unsetParentSBMLObject ()
	Unsets the parent SBML object. More...

int	unsetStyle ()
	Unsets the MathML style 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::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_UNKNOWN. If the type isn't supplied when caling this constructor, the caller should set the node type to something else as soon as possible usingsetType().

Parameters

type	an optional ASTNodeType_t code indicating the type of node to create.

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

token the Token to add.

ASTNode::ASTNode ( const ASTNode & orig )

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

Parameters

orig	the ASTNode to be copied.

ASTNode::~ASTNode ( )

virtual

Destroys this ASTNode, including any child nodes.

Member Function Documentation

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

disownedChild	the ASTNode instance to add
inRead	hack used for representsBVar function to be correct

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Warning: Explicitly adding, removing or replacing children of an ASTNode object may change the structure of the mathematical formula it represents, and may even render the representation invalid. Callers need to be careful to use this method in the context of other operations to create complete and correct formulas. The methodASTNode::isWellFormedASTNode() may also be useful for checking the results of node modifications.

See also: prependChild(ASTNode* disownedChild); replaceChild(unsigned int n, ASTNode* disownedChild); insertChild(unsigned int n, ASTNode* disownedChild); removeChild(unsigned int n); isWellFormedASTNode()

Examples:: createExampleSBML.cpp.

int ASTNode::addSemanticsAnnotation ( XMLNode * disownedAnnotation )

Adds the given XMLNode as a semantic annotation of 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

disownedAnnotation the annotation to add.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Note: Although SBML permits the semantic annotation construct in MathML expressions, the truth is that this construct has so far (at this time of this writing, which is early 2011) seen very little use in SBML software. The full implications of using semantic 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@caltech.edu and/or sbml-interoperability@caltech.edu.

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:

If the node type is AST_NAME and the node name matches "ExponentialE", "Pi", "True" or "False" the node type is converted to the corresponding AST_CONSTANT_X type.
If the node type is an AST_FUNCTION and the node name matches an SBML (MathML) function name, logical operator name, or relational operator name, the node is converted to the corresponding AST_FUNCTION_X or AST_LOGICAL_X type.

SBML Level 1 function names are searched first; thus, for example, canonicalizing log will result in a node type of AST_FUNCTION_LN. (See the SBML Level 1 Version 2 Specification, Appendix C.)

Sometimes, canonicalization of a node results in a structural conversion of the node as a result of adding a child. For example, a node with the SBML Level 1 function name sqr and a single child node (the argument) will be transformed to a node of type AST_FUNCTION_POWER with two children. The first child will remain unchanged, but the second child will be an ASTNode of type AST_INTEGER and a value of 2. The function names that result in structural changes are: log10, sqr, and sqrt.

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.

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 (non-zero).

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 non-zero represents true and zero represents false.

Parameters

predicate	the predicate to use.
lst	the List to which ASTNode objects should be added.

See also: getListOfNodes(ASTNodePredicate predicate) const

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_UNKNOWN. This method has no effect on other types of nodes.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

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

ASTBasePlugin* ASTNode::getASTPlugin ( ASTNodeType_t type )

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

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

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

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

char ASTNode::getCharacter ( ) const

Gets the value of this node as a single character.

This function should be called only when getType() returns AST_PLUS, AST_MINUS, AST_TIMES, AST_DIVIDE or AST_POWER.

Returns: the value of this ASTNode as a single character

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

Gets a child of this node according to its index number.

Parameters

n	the 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.

std::string ASTNode::getClass ( ) const

Gets the class of this ASTNode.

Returns: the MathML class of this ASTNode.

XMLAttributes * ASTNode::getDefinitionURL ( ) const

Gets the MathML "definitionURL" attribute value.

Returns: the value of the definitionURL attribute, in the form of a libSBML XMLAttributes object.

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)

long ASTNode::getDenominator ( ) const

Gets the value of the denominator of this node.

This function should be called only when getType() == AST_RATIONAL.

Returns: the value of the denominator of this ASTNode.

long ASTNode::getExponent ( ) const

Gets the exponent value of this ASTNode.

This function should be called only when getType() returns AST_REAL_E or AST_REAL.

Returns: the value of the exponent of this ASTNode.

std::string ASTNode::getId ( ) const

Gets the id of this ASTNode.

Returns: the MathML id of this ASTNode.

long ASTNode::getInteger ( ) const

Gets the value of this node as an integer.

This function should be called only when getType() == AST_INTEGER.

Returns: the value of this ASTNode as a (long) integer.

ASTNode * ASTNode::getLeftChild ( ) const

Gets 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.

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 (non-zero).

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

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

where a return value of non-zero represents true and zero represents false.

Parameters

predicate the predicate to use

Returns: the list of nodes for which the predicate returned true (non-zero). 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.

double ASTNode::getMantissa ( ) const

Gets the mantissa value of this node.

This function should be called only when getType() returns AST_REAL_E or AST_REAL. If getType() returns AST_REAL, this method is identical to getReal().

Returns: the value of the mantissa of this ASTNode.

const char * ASTNode::getName ( ) const

Gets 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 false.

Returns: the value of this ASTNode as a string.

unsigned int ASTNode::getNumChildren ( ) const

Gets the number of children that this node has.

Returns: the number of children of this ASTNode, or 0 is this node has no children.

Examples:: printMath.cpp.

long ASTNode::getNumerator ( ) const

Gets the value of the numerator of this node.

This function should be called only when getType() == AST_RATIONAL.

Returns: the value of the numerator of this ASTNode.

unsigned int ASTNode::getNumSemanticsAnnotations ( ) const

Gets the number of semantic annotation elements inside 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.

See also: ASTNode::addSemanticsAnnotation(XMLNode* disownedAnnotation)

const char * ASTNode::getOperatorName ( ) const

Gets 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).

SBase * ASTNode::getParentSBMLObject ( ) const

Returns the parent SBML object.

Returns: the parent SBML object of this ASTNode.

int ASTNode::getPrecedence ( ) const

Gets 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

double ASTNode::getReal ( ) const

Gets the real-numbered value of this node.

This function should be called only when isReal() == true.

This function performs the necessary arithmetic if the node type is AST_REAL_E (mantissa * 10^exponent) or AST_RATIONAL (numerator / denominator).

Returns: the value of this ASTNode as a real (double).

ASTNode * ASTNode::getRightChild ( ) const

Gets 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.

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

Gets the nth semantic annotation of 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 nth annotation of this ASTNode, or NULL if this node has no nth annotation (n > getNumSemanticsAnnotations() - 1).

See also: ASTNode::addSemanticsAnnotation(XMLNode* disownedAnnotation)

std::string ASTNode::getStyle ( ) const

Gets the style of this ASTNode.

Returns: the MathML style of this ASTNode.

ASTNodeType_t ASTNode::getType ( ) const

Gets the type of this ASTNode.

The value returned is one of the enumeration values such as AST_LAMBDA, AST_PLUS, etc.

Returns: the type of this ASTNode.

std::string ASTNode::getUnits ( ) const

Gets 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()

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: ASTNode::setUserData

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_PI, AST_CONSTANT_E, or AST_NAME_AVOGADRO, or 1 for nodes of type AST_CONSTANT_TRUE and 0 for nodes of type AST_CONSTANT_FALSE. It does not evaluate the node in any way so, for example, it will not return the value of a named ASTNode_t or attempt to evaluate a function. This includes a node representing time i.e. nodes of type AST_NAME_TIME.

bool ASTNode::hasCorrectNumberArguments ( ) const

Returns true or false depending on whether this ASTNode has the correct number of children for its type.

For example, an ASTNode with type AST_PLUS expects 2 child nodes.

Note: This function performs a check on the top-level node only. Child nodes are not checked.

Returns: true if this ASTNode has the appropriate number of children for its type, false otherwise.

See also: isWellFormedASTNode()

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

Returns true if this node is of type.

Parameters

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.

bool ASTNode::hasUnits ( ) const

Returns true (non-zero) 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.

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

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

Parameters

n	unsigned int the index of the ASTNode being added
disownedChild	ASTNode to insert as the nth child

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Warning: Explicitly adding, removing or replacing children of an ASTNode object may change the structure of the mathematical formula it represents, and may even render the representation invalid. Callers need to be careful to use this method in the context of other operations to create complete and correct formulas. The methodASTNode::isWellFormedASTNode() may also be useful for checking the results of node modifications.

See also: addChild(ASTNode* disownedChild); prependChild(ASTNode* disownedChild); replaceChild(unsigned int n, ASTNode* disownedChild); removeChild(unsigned int n)

bool ASTNode::isAvogadro ( ) const

Returns true (non-zero) if this node is the special symbol avogadro.

The predicate returns false (zero) otherwise.

Returns: true if this ASTNode is the special symbol avogadro.

See also: SBML_parseL3Formula()

bool ASTNode::isBoolean ( ) const

Returns true (non-zero) if this node has a boolean type (a logical operator, a relational operator, or the constants true or false).

Returns: true if this ASTNode is a boolean, false otherwise.

bool ASTNode::isCiNumber ( ) const

Returns true (non-zero) 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.

bool ASTNode::isConstant ( ) const

Returns true (non-zero) 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 AST_NAME_AVOGADRO in SBML Level 3.

bool ASTNode::isConstantNumber ( ) const

Returns true (non-zero) 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_AVOGADRO in SBML Level 3.

bool ASTNode::isCSymbolFunction ( ) const

Returns true (non-zero) if this node represents a MathML csymbol representing a function.

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

bool ASTNode::isFunction ( ) const

Returns true (non-zero) if this node represents a MathML function (e.g., abs()), or an SBML Level 1 function, or a user-defined function.

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

bool ASTNode::isInfinity ( ) const

Returns true (non-zero) 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.

bool ASTNode::isInteger ( ) const

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

Returns: true if this ASTNode is of type AST_INTEGER, false otherwise.

bool ASTNode::isLambda ( ) const

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

Returns: true if this ASTNode is of type AST_LAMBDA, false otherwise.

bool ASTNode::isLog10 ( ) const

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

More precisely, this predicate returns true if the node type is AST_FUNCTION_LOG with two children, the first of which is an AST_INTEGER equal to 10.

Returns: true if the given ASTNode represents a log10() function, false otherwise.

See also: SBML_parseL3Formula()

bool ASTNode::isLogical ( ) const

Returns true (non-zero) if this node is a MathML logical operator (i.e., and, or, not, xor).

Returns: true if this ASTNode is a MathML logical operator

bool ASTNode::isName ( ) const

Returns true (non-zero) if this node is a user-defined variable name in SBML L1, L2 (MathML), or the special symbols time or avogadro.

The predicate returns false (zero) otherwise.

Returns: true if this ASTNode is a user-defined variable name in SBML L1, L2 (MathML) or the special symbols delay or time.

bool ASTNode::isNaN ( ) const

Returns true (non-zero) 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.

bool ASTNode::isNegInfinity ( ) const

Returns true (non-zero) 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.

bool ASTNode::isNumber ( ) const

Returns true (non-zero) 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.

bool ASTNode::isOperator ( ) const

Returns true (non-zero) if this node is a mathematical operator, meaning, +, -, *, / or ^ (power).

Returns: true if this ASTNode is an operator.

bool ASTNode::isPiecewise ( ) const

Returns true (non-zero) if this node is the MathML <piecewise> construct, false (zero) otherwise.

Returns: true if this ASTNode is a MathML piecewise function

bool ASTNode::isRational ( ) const

Returns true (non-zero) if this node represents a rational number, false (zero) otherwise.

Returns: true if this ASTNode is of type AST_RATIONAL.

bool ASTNode::isReal ( ) const

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

More precisely, this node must be of one of the following types: AST_REAL, AST_REAL_E or AST_RATIONAL.

Returns: true if the value of this ASTNode can represented as a real number, false otherwise.

bool ASTNode::isRelational ( ) const

Returns true (non-zero) if this node is a MathML relational operator, meaning ==, >=, >, <, and !=.

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

bool ASTNode::isSetClass ( ) const

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

Returns: true if this ASTNode has an attribute class, false otherwise.

bool ASTNode::isSetId ( ) const

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

Returns: true if this ASTNode has an attribute id, false otherwise.

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()

bool ASTNode::isSetStyle ( ) const

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

Returns: true if this ASTNode has an attribute style, false otherwise.

bool ASTNode::isSetUnits ( ) const

Returns true (non-zero) 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.

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: ASTNode::setUserData(); ASTNode::getUserData(); ASTNode::unsetUserData()

bool ASTNode::isSqrt ( ) const

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

More precisely, the node type must be AST_FUNCTION_ROOT with two children, the first of which is an AST_INTEGER node having value equal to 2.

Returns: true if the given ASTNode represents a sqrt() function, false otherwise.

bool ASTNode::isUMinus ( ) const

Returns true (non-zero) 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_MINUS and has exactly one child.

For numbers, unary minus nodes can be "collapsed" by negating the number. In fact, SBML_parseFormula() does this during its parsing process, and SBML_parseL3Formula() has a configuration option that allows this behavior to be turned on or off. However, unary minus nodes for symbols (AST_NAME) cannot be "collapsed", so this predicate function is necessary.

Returns: true if this ASTNode is a unary minus, false otherwise.

See also: SBML_parseL3Formula()

bool ASTNode::isUnknown ( ) const

Returns true (non-zero) if this node has an unknown type.

"Unknown" nodes have the type AST_UNKNOWN. Nodes with unknown types will not appear in an ASTNode tree returned by libSBML based upon valid SBML input; the only situation in which a node with type AST_UNKNOWN may appear is immediately after having create a new, untyped node using the ASTNode constructor. Callers creating nodes should endeavor to set the type to a valid node type as soon as possible after creating new nodes.

Returns: true if this ASTNode is of type AST_UNKNOWN, false otherwise.

bool ASTNode::isUPlus ( ) const

Returns true (non-zero) 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_MINUS and has exactly one child.

Returns: true if this ASTNode is a unary plus, false otherwise.

bool ASTNode::isUserFunction ( ) const

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

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

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()

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

Assignment operator for ASTNode.

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

disownedChild the ASTNode instance to add

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Warning: Explicitly adding, removing or replacing children of an ASTNode object may change the structure of the mathematical formula it represents, and may even render the representation invalid. Callers need to be careful to use this method in the context of other operations to create complete and correct formulas. The methodASTNode::isWellFormedASTNode() may also be useful for checking the results of node modifications.

See also: addChild(ASTNode* disownedChild); replaceChild(unsigned int n, ASTNode* disownedChild); insertChild(unsigned int n, ASTNode* disownedChild); removeChild(unsigned int n)

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.

int ASTNode::removeChild ( unsigned int n )

Removes the nth child of this ASTNode object.

Parameters

n	unsigned int the index of the child to remove

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Warning: Explicitly adding, removing or replacing children of an ASTNode object may change the structure of the mathematical formula it represents, and may even render the representation invalid. Callers need to be careful to use this method in the context of other operations to create complete and correct formulas. The methodASTNode::isWellFormedASTNode() may also be useful for checking the results of node modifications.

See also: addChild(ASTNode* disownedChild); prependChild(ASTNode* disownedChild); replaceChild(unsigned int n, ASTNode* disownedChild); insertChild(unsigned int n, ASTNode* disownedChild)

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

virtual

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

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 in MathML <cn> elements.)

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

Replaces occurences of a given name within this ASTNode with the name/value/formula represented by arg.

For example, if the formula in this ASTNode is x + y, then the <bvar> is x and arg is an ASTNode representing the real value 3. This method substitutes 3 for x within this ASTNode object.

Parameters

bvar	a string representing the variable name to be substituted
arg	an ASTNode representing the name/value/formula to substitute

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

n	unsigned int the index of the child to replace
disownedChild	ASTNode to replace the nth child
delreplaced	boolean indicating whether to delete the replaced child.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Warning: Explicitly adding, removing or replacing children of an ASTNode object may change the structure of the mathematical formula it represents, and may even render the representation invalid. Callers need to be careful to use this method in the context of other operations to create complete and correct formulas. The methodASTNode::isWellFormedASTNode() may also be useful for checking the results of node modifications.

See also: addChild(ASTNode* disownedChild); prependChild(ASTNode* disownedChild); insertChild(unsigned int n, ASTNode* disownedChild); removeChild(unsigned int n)

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

Returns true (non-zero) 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.

See also: isBoolean()

Returns: true if this ASTNode returns a boolean, false otherwise.

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_UNKNOWN.

Parameters

value the character value to which the node's value should be set.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

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

Sets the MathML class of this ASTNode to className.

Parameters

className string representing the MathML class for this node.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

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

Sets the MathML id of this ASTNode to id.

Parameters

id	`string` representing the identifier.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

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_NAME if (and only if) the ASTNode was previously an operator ( isOperator() == true), number ( isNumber() == true), or unknown. This allows names to be set for AST_FUNCTION nodes and the like.

Parameters

name	the string containing the name to which this node's value should be set

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

Examples:: createExampleSBML.cpp.

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

Sets the MathML style of this ASTNode to style.

Parameters

style string representing the identifier.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int ASTNode::setType ( ASTNodeType_t type )

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

Parameters

type	the type to which this node should be set

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Note: A side-effect of doing this is that any numerical values previously stored in this node are reset to zero.

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

units string representing the unit identifier.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Note: The sbml:units attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.

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

userData specifies the new user data.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int ASTNode::setValue ( int value )

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

Parameters

value the integer to which this node's value should be set

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int ASTNode::setValue ( long value )

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

Parameters

value the integer to which this node's value should be set

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

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_RATIONAL.

Parameters

numerator	the numerator value of the rational
denominator	the denominator value of the rational

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int ASTNode::setValue ( double value )

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

This is functionally equivalent to:

setValue(value, 0);

Parameters

value the double format number to which this node's value should be set

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

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_E.

Parameters

mantissa	the mantissa of this node's real-numbered value
exponent	the exponent of this node's real-numbered value

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int ASTNode::swapChildren ( ASTNode * that )

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

Parameters

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

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int ASTNode::unsetClass ( )

Unsets the MathML class of this ASTNode.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int ASTNode::unsetId ( )

Unsets the MathML id of this ASTNode.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int ASTNode::unsetParentSBMLObject ( )

Unsets the parent SBML object.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: isSetParentSBMLObject(); getParentSBMLObject()

int ASTNode::unsetStyle ( )

Unsets the MathML style of this ASTNode.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int ASTNode::unsetUnits ( )

Unsets the units of this ASTNode.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

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.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

See also: ASTNode::setUserData(); ASTNode::getUserData(); ASTNode::isSetUserData()

Detailed Description

ASTNodeType_t

Converting between ASTs and text strings

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation