Inheritance diagram for libsbmlcs.ASTNode:

Detailed Description

{core}

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

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

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

*

An AST node in libSBML is a recursive structure containing a pointer to the node's value (which might be, for example, a number or a symbol) and a list of children nodes. Each ASTNode node may have none, one, two, or more children depending on its type. 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 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
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 the applications can use the text-string based translation functions such as . 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.

Finally, it is worth noting that the AST and MathML handling code in libSBML remains written in C, not C++. (All of libSBML was originally written in C.) Readers may occasionally wonder why some aspects are more C-like and less object oriented, and that's one of the reasons.

The set of possible ASTNode types

*

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 a set of static integer constants defined in the class libsbml. Their names begin with the characters AST_. 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_COT	AST_LOGICAL_NOT
AST_CONSTANT_FALSE	AST_FUNCTION_COTH	AST_LOGICAL_OR
AST_CONSTANT_PI	AST_FUNCTION_CSC	AST_LOGICAL_XOR
AST_CONSTANT_TRUE	AST_FUNCTION_CSCH	AST_MINUS
AST_DIVIDE	AST_FUNCTION_DELAY	AST_NAME
AST_FUNCTION	AST_FUNCTION_EXP	AST_NAME_AVOGADRO (Level 3 only)
AST_FUNCTION_ABS	AST_FUNCTION_FACTORIAL	AST_NAME_TIME
AST_FUNCTION_ARCCOS	AST_FUNCTION_FLOOR	AST_PLUS
AST_FUNCTION_ARCCOSH	AST_FUNCTION_LN	AST_POWER
AST_FUNCTION_ARCCOT	AST_FUNCTION_LOG	AST_RATIONAL
AST_FUNCTION_ARCCOTH	AST_FUNCTION_PIECEWISE	AST_REAL
AST_FUNCTION_ARCCSC	AST_FUNCTION_POWER	AST_REAL_E
AST_FUNCTION_ARCCSCH	AST_FUNCTION_ROOT	AST_RELATIONAL_EQ
AST_FUNCTION_ARCSEC	AST_FUNCTION_SEC	AST_RELATIONAL_GEQ
AST_FUNCTION_ARCSECH	AST_FUNCTION_SECH	AST_RELATIONAL_GT
AST_FUNCTION_ARCSIN	AST_FUNCTION_SIN	AST_RELATIONAL_LEQ
AST_FUNCTION_ARCSINH	AST_FUNCTION_SINH	AST_RELATIONAL_LT
AST_FUNCTION_ARCTAN	AST_FUNCTION_TAN	AST_RELATIONAL_NEQ
AST_FUNCTION_ARCTANH	AST_FUNCTION_TANH	AST_TIMES
AST_FUNCTION_CEILING	AST_INTEGER	AST_UNKNOWN
AST_FUNCTION_COS	AST_LAMBDA
AST_FUNCTION_COSH	AST_LOGICAL_AND

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.

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 bylibsbmlcs.libsbml.formulaToString()and read bylibsbmlcs.libsbml.parseFormula() and SBML_parseL3Formula() are in a simple C-inspired infix notation. A formula in one of these two text-string formats can be handed to a program that understands SBML mathematical expressions, or used as part of a translation system. The libSBML distribution comes with example programs in the 'examples' subdirectory that demonstrate such things as translating infix formulas into MathML and vice-versa.

Please see the documentation for the functions libsbmlcs.libsbml.parseFormula() and SBML_parseL3Formula() for detailed explanations of the infix syntax they accept.

See also: SBML_parseL3Formula(); libsbmlcs.libsbml.parseFormula(); libsbmlcs.libsbml.formulaToString()

Public Member Functions
int	addChild (ASTNode child)
	Adds the given node as a child of this ASTNode. More...

void	addExpectedAttributes (SWIGTYPE_p_ExpectedAttributes attributes, XMLInputStream stream)

void	addPlugin (ASTBasePlugin plugin)

int	addSemanticsAnnotation (XMLNode sAnnotation)
	Adds the given XMLNode as a MathML. More...

	ASTNode (int type)
	Creates a new ASTNode. More...

	ASTNode (SBMLNamespaces sbmlns, int type)

	ASTNode ()

	ASTNode (SBMLNamespaces sbmlns)

	ASTNode (ASTNode orig)
	Copy constructor; creates a deep copy of the given ASTNode. More...

bool	canonicalize ()
	Converts this ASTNode to a canonical form. More...

ASTBase	deepCopy ()
	Creates a recursive copy of this node and all its children. More...

override void	Dispose ()

override bool	Equals (Object sb)

int	freeName ()
	Frees the name of this ASTNode and sets it to `null`. More...

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

ASTNode	getChild (long n)
	Returns the child at index n of this node. More...

string	getClass ()
	Returns the MathML `class` attribute value of this ASTNode. More...

XMLAttributes	getDefinitionURL ()
	Returns the MathML `definitionURL` attribute value. More...

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

int	getDenominator ()
	Returns the value of the denominator of this node. More...

int	getExponent ()
	Returns the exponent value of this ASTNode. More...

int	getExtendedType ()
	Returns the extended type of this ASTNode. More...

ASTBase	getFunction ()

override int	GetHashCode ()

string	getId ()
	Returns the MathML `id` attribute value of this ASTNode. More...

int	getInteger ()
	Returns the value of this node as an integer. More...

ASTNode	getLeftChild ()
	Returns the left child of this node. More...

ASTNodeList	getListOfNodes ()

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

string	getName ()
	Returns the value of this node as a string. More...

string	getNameFromType (int type)

long	getNumBvars ()

long	getNumChildren ()
	Returns the number of children of this node. More...

int	getNumerator ()
	Returns the value of the numerator of this node. More...

long	getNumPlugins ()
	Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...

long	getNumSemanticsAnnotations ()
	Returns the number of MathML. More...

string	getOperatorName ()
	Returns the value of this operator node as a string. More...

string	getPackageName ()

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

ASTBasePlugin	getPlugin (string package)
	Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More...

ASTBasePlugin	getPlugin (long n)
	Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More...

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

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

ASTNode	getRightChild ()
	Returns the right child of this node. More...

XMLNode	getSemanticsAnnotation (long n)
	Returns the nth MathML. More...

string	getStyle ()
	Returns the MathML `style` attribute value of this ASTNode. More...

int	getType ()
	Returns the type of this ASTNode. More...

int	getTypeCode ()

int	getTypeFromName (string name)

string	getUnits ()
	Returns the units of this ASTNode. More...

string	getUnitsPrefix ()

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

bool	hasCnUnits ()

bool	hasCorrectNumberArguments ()
	Returns `true` if this ASTNode has the correct number of children for its type. More...

int	hasTypeAndNumChildren (int type, long numchildren)
	Returns `true` if this node is of a certain type with a specific number of children. More...

bool	hasUnits ()
	Returns `true` if this node or any of its children nodes have the attribute. More...

int	insertChild (long n, ASTNode newChild)
	Inserts the given ASTNode node at a given point in the current ASTNode's list of children. More...

bool	isAvogadro ()
	Returns `true` if this node represents the predefined value for Avogadro's constant. More...

bool	isBinaryFunction ()

bool	isBoolean ()
	Returns `true` if this node has a Boolean type. More...

bool	isChild ()

bool	isCiNumber ()

bool	isConstant ()
	Returns `true` if this node represents a MathML constant. More...

bool	isConstantNumber ()

bool	isCSymbolFunction ()

bool	isCSymbolNumber ()

bool	isExponential ()

bool	isFunction ()
	Returns `true` if this node represents a function. More...

bool	isFunctionNode ()

bool	isInfinity ()
	Returns `true` if this node represents the special IEEE 754 value for infinity. More...

bool	isInteger ()
	Returns `true` if this node contains an integer value. More...

bool	isLambda ()
	Returns `true` if this node is a MathML. More...

bool	isLog10 ()
	Returns `true` if this node represents a `log10` function. More...

bool	isLogical ()
	Returns `true` if this node is a MathML logical operator. More...

bool	isName ()
	Returns `true` if this node is a user-defined variable name or the symbols for time or Avogadro's constant. More...

bool	isNaN ()
	Returns `true` if this node represents the special IEEE 754 value 'not a number' (NaN). More...

bool	isNaryFunction ()

bool	isNegInfinity ()
	Returns `true` if this node represents the special IEEE 754 value 'negative infinity'. More...

bool	isNumber ()
	Returns `true` if this node contains a number. More...

bool	isNumberNode ()

bool	isOperator ()
	Returns `true` if this node is a mathematical operator. More...

bool	isPiecewise ()
	Returns `true` if this node is the MathML. More...

bool	isQualifier ()
	Predicate returning `true` if this node is a MathML qualifier. More...

bool	isRational ()
	Returns `true` if this node represents a rational number. More...

bool	isReal ()
	Returns `true` if this node can represent a real number. More...

bool	isRelational ()
	Returns `true` if this node is a MathML relational operator. More...

bool	isSemantics ()
	Predicate returning `true` if this node is a MathML semantics node. More...

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

bool	isSetId ()
	Returns `true` if this node has a value for the MathML attribute `id`. More...

bool	isSetParentSBMLObject ()
	Returns `true` if this node has a value for the parent SBML object. More...

bool	isSetStyle ()
	Returns `true` if this node has a value for the MathML attribute `style`. More...

bool	isSetType ()

bool	isSetUnits ()
	Returns `true` if this node has the attribute. More...

bool	isSetUserData ()
	Returns `true` if this node has a user data object. More...

bool	isSqrt ()
	Returns `true` if this node represents a square root function. More...

bool	isTopLevelMathMLFunctionNodeTag (string name)

bool	isTopLevelMathMLNumberNodeTag (string name)

bool	isUMinus ()
	Returns `true` if this node is a unary minus operator. More...

bool	isUnaryFunction ()

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

bool	isUPlus ()
	Returns `true` if this node is a unary plus operator. More...

bool	isUserFunction ()

bool	isWellFormedASTNode ()
	Returns `true` or `false` depending on whether this ASTNode is well-formed. More...

bool	isWellFormedNode ()

void	loadASTPlugins (SBMLNamespaces sbmlns)

void	logError (XMLInputStream stream, XMLToken element, int code, string msg)

void	logError (XMLInputStream stream, XMLToken element, int code)

int	prependChild (ASTNode child)
	Adds the given node as a child of this ASTNode. More...

bool	read (XMLInputStream stream, string reqd_prefix)

bool	read (XMLInputStream stream)

bool	readAttributes (XMLAttributes attributes, SWIGTYPE_p_ExpectedAttributes expectedAttributes, XMLInputStream stream, XMLToken element)

void	reduceToBinary ()
	Reduces this ASTNode to a binary tree. More...

int	removeChild (long n)
	Removes the nth child of this ASTNode object. More...

void	renameSIdRefs (string oldid, string newid)
	Renames all the SIdRef attributes on this node and its child nodes. More...

void	renameUnitSIdRefs (string oldid, string newid)
	Renames all the UnitSIdRef attributes on this node and its child nodes. More...

void	replaceArgument (string bvar, ASTNode arg)
	Replaces occurrences of a given name with a given ASTNode. More...

int	replaceChild (long n, ASTNode newChild)
	Replaces the nth child of this ASTNode with the given ASTNode. More...

void	replaceIDWithFunction (string id, ASTNode function)
	Replace any nodes of type AST_NAME with the name 'id' from the child 'math' object with the provided ASTNode. More...

bool	returnsBoolean (Model model)
	Returns `true` if this node returns a Boolean value. More...

bool	returnsBoolean ()
	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 (string className)
	Sets the MathML attribute `class` of this ASTNode. More...

int	setDefinitionURL (XMLAttributes url)
	Sets the MathML attribute `definitionURL`. More...

int	setDefinitionURL (string url)
	Sets the MathML attribute `definitionURL`. More...

int	setId (string id)
	Sets the MathML attribute `id` of this ASTNode. More...

void	setIsChildFlag (bool flag)

int	setName (string name)
	Sets the value of this ASTNode to the given name. More...

int	setPackageName (string name)

int	setStyle (string style)
	Sets the MathML attribute `style` of this ASTNode. More...

int	setType (int type)
	Sets the type of this ASTNode to the given type code. More...

int	setUnits (string units)
	Sets the units of this ASTNode to units. More...

int	setUserData (SWIGTYPE_p_void userData)

int	setValue (int value)
	Sets the value of this ASTNode to the given (`long`) integer. More...

int	setValue (int numerator, int 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, int 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...

void	write (XMLOutputStream stream)

void	writeNodeOfType (XMLOutputStream stream, int type, bool inChildNode)

void	writeNodeOfType (XMLOutputStream stream, int type)

Static Public Member Functions
static bool	operator!= (ASTNode lhs, ASTNode rhs)

static bool	operator== (ASTNode lhs, ASTNode rhs)

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.ASTNode.ASTNode ( int type )

Creates 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 using ASTNode::setType(int).

Parameters

type	an optional typecode indicating the type of node to create.

libsbmlcs.ASTNode.ASTNode	(	SBMLNamespaces	sbmlns,
		int	type
	)

libsbmlcs.ASTNode.ASTNode ( )

libsbmlcs.ASTNode.ASTNode ( SBMLNamespaces sbmlns )

libsbmlcs.ASTNode.ASTNode ( ASTNode orig )

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

Parameters

orig	the ASTNode to be copied.

Member Function Documentation

int libsbmlcs.ASTNode.addChild ( ASTNode child )

Adds the given node as a child of this ASTNode.

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

Parameters

child the ASTNode instance to add

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

*

Warning: Explicitly adding, removing or replacing children of an ASTNode objectmay 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 method ASTNode::isWellFormedASTNode()may also be useful for checking the results of node modifications.

See also: prependChild(ASTNode child); replaceChild(long n, ASTNode child); insertChild(long n, ASTNode child); removeChild(long n); isWellFormedASTNode()

void libsbmlcs.ASTBase.addExpectedAttributes	(	SWIGTYPE_p_ExpectedAttributes	attributes,
		XMLInputStream	stream
	)

inherited

void libsbmlcs.ASTBase.addPlugin ( ASTBasePlugin plugin )

inherited

int libsbmlcs.ASTNode.addSemanticsAnnotation ( XMLNode sAnnotation )

Adds the given XMLNode as a MathML.

<semantics> element to this ASTNode.

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

Parameters

sAnnotation the annotation to add.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

*

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: ASTNode::getNumSemanticsAnnotations(); ASTNode::getSemanticsAnnotation()

bool libsbmlcs.ASTNode.canonicalize ( )

Converts this ASTNode to a canonical form.

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.

Returns: true if this node was successfully converted to canonical form, false otherwise.

ASTBase libsbmlcs.ASTNode.deepCopy ( )

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.

override void libsbmlcs.ASTNode.Dispose ( )

virtual

Reimplemented from libsbmlcs.ASTBase.

override bool libsbmlcs.ASTNode.Equals ( Object sb )

int libsbmlcs.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 possible values returned by this function are:

char libsbmlcs.ASTNode.getCharacter ( )

Returns the value of this node as a single character.

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

Returns: the value of this ASTNode as a single character

ASTNode libsbmlcs.ASTNode.getChild ( long n )

Returns the child at index n of this node.

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 > ASTNode::getNumChildren()- 1).

See also: getNumChildren(); getLeftChild(); getRightChild()

string libsbmlcs.ASTNode.getClass ( )

Returns the MathML class attribute value of this ASTNode.

Returns: the MathML class of this ASTNode, if any exists.

See also: isSetClass(); setClass(); unsetClass()

XMLAttributes libsbmlcs.ASTNode.getDefinitionURL ( )

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(string url); getDefinitionURLString()

string libsbmlcs.ASTNode.getDefinitionURLString ( )

Returns the MathML definitionURL attribute value as a string.

Returns: the value of the definitionURL attribute, as a string.

See also: getDefinitionURL(); setDefinitionURL(string url); setDefinitionURL(XMLAttributes url)

int libsbmlcs.ASTNode.getDenominator ( )

Returns the value of the denominator of this node.

Returns: the value of the denominator of this ASTNode, or 1 if this node has no numerical value.

Note: This function should be called only when ASTNode::getType()returns AST_RATIONAL. It will return 1 if the node type is another type, but since 1 may be a valid value for the denominator of a rational number, it is important to be sure that the node type is the correct type in order to correctly interpret the returned value.

int libsbmlcs.ASTNode.getExponent ( )

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 AST_REAL_E. It will return 0 if the node type is another type, but since 0 may be a valid value, it is important to be sure that the node type is the correct type in order to correctly interpret the returned value.

int libsbmlcs.ASTNode.getExtendedType ( )

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 AST_ORIGINATES_IN_PACKAGE and getExtendedType() will return a package-specific type code. To find out the possible package-specific types (if any), please consult the documentation for the particular package.

See also: getType()

ASTBase libsbmlcs.ASTBase.getFunction ( )

inherited

override int libsbmlcs.ASTNode.GetHashCode ( )

string libsbmlcs.ASTNode.getId ( )

Returns the MathML id attribute value of this ASTNode.

Returns: the MathML id of this ASTNode.

See also: isSetId(); setId(); unsetId()

int libsbmlcs.ASTNode.getInteger ( )

Returns the value of this node as an integer.

If this node type is AST_RATIONAL, this method returns the value of the numerator.

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

Note: This function should be called only when ASTNode::getType()returns AST_INTEGER or AST_RATIONAL. It will return 0 if the node type is not one of these, but since 0 may be a valid value for integer, it is important to be sure that the node type is one of the expected types in order to understand if 0 is the actual value.

ASTNode libsbmlcs.ASTNode.getLeftChild ( )

Returns the left child of this node.

Returns: the left child of this ASTNode. This is equivalent to calling ASTNode::getChild(long)with an argument of 0.

See also: getNumChildren(); getChild(); getRightChild()

ASTNodeList libsbmlcs.ASTNode.getListOfNodes ( )

double libsbmlcs.ASTNode.getMantissa ( )

Returns the mantissa value of this node.

If ASTNode::getType()returns AST_REAL, this method is identical to ASTNode::getReal().

Returns: the value of the mantissa of this ASTNode, or 0 if this node is not a type that has a real-numbered value.

Note: This function should be called only when ASTNode::getType()returns AST_REAL_E, AST_REAL or AST_NAME_AVOGADRO. It will return 0 if the node type is another type, but since 0 may be a valid value, it is important to be sure that the node type is the correct type in order to correctly interpret the returned value.

string libsbmlcs.ASTNode.getName ( )

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).

string libsbmlcs.ASTBase.getNameFromType ( int type )

inherited

long libsbmlcs.ASTNode.getNumBvars ( )

long libsbmlcs.ASTNode.getNumChildren ( )

Returns the number of children of this node.

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

int libsbmlcs.ASTNode.getNumerator ( )

Returns the value of the numerator of this node.

This function should be called only when ASTNode::getType()returns AST_RATIONAL or AST_INTEGER.

Returns: the value of the numerator of this ASTNode.

long libsbmlcs.ASTBase.getNumPlugins ( )

inherited

Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.

Returns: the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.

long libsbmlcs.ASTNode.getNumSemanticsAnnotations ( )

Returns the number of MathML.

<semantics> element elements on this node.

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

Returns: the number of annotations of this ASTNode.

*

Note: Although SBML permits the use of the MathML <semantics> annotation construct, the truth is that this construct has so far (at this time of this writing, which is early 2014) seen very little use in SBML software. The full implications of using these annotations are still poorly understood. If you wish to use this construct, we urge you to discuss possible uses and applications on the SBML discussion lists, particularly sbml-discuss and/or sbml-interoperability.

See also: ASTNode::addSemanticsAnnotation(); ASTNode::getSemanticsAnnotation()

string libsbmlcs.ASTNode.getOperatorName ( )

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).

string libsbmlcs.ASTNode.getPackageName ( )

SBase libsbmlcs.ASTNode.getParentSBMLObject ( )

Returns the parent SBML object.

Returns: the parent SBML object of this ASTNode.

See also: isSetParentSBMLObject(); setParentSBMLObject()

ASTBasePlugin libsbmlcs.ASTBase.getPlugin ( string package )

inherited

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

Parameters

package the name or URI of the package

Returns: the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

ASTBasePlugin libsbmlcs.ASTBase.getPlugin ( long n )

inherited

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

Parameters

n	the index of the plug-in to return

Returns: the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

int libsbmlcs.ASTNode.getPrecedence ( )

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

double libsbmlcs.ASTNode.getReal ( )

Returns the real-numbered value of this node.

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), or 0 if this is not a node that holds a number.

Note: This function should be called only when this ASTNode has a numerical value type. It will return 0 if the node type is another type, but since 0 may be a valid value, it is important to be sure that the node type is the correct type in order to correctly interpret the returned value.

ASTNode libsbmlcs.ASTNode.getRightChild ( )

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()

XMLNode libsbmlcs.ASTNode.getSemanticsAnnotation ( long n )

Returns the nth MathML.

<semantics> element on this ASTNode.

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

Parameters

n	the 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: ASTNode::addSemanticsAnnotation(); ASTNode::getNumSemanticsAnnotations()

string libsbmlcs.ASTNode.getStyle ( )

Returns the MathML style attribute value of this ASTNode.

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

See also: isSetStyle(); setStyle(); unsetStyle()

int libsbmlcs.ASTNode.getType ( )

Returns the type of this ASTNode.

The value returned is one of the Core AST type codes such as AST_LAMBDA, AST_PLUS, etc.

Returns: the type of this ASTNode.

Note: The introduction of extensibility in SBML Level 3 brings with it a need to allow for the possibility of node types that are defined by plug-ins implementing SBML Level 3 packages. If a given ASTNode is a construct created by a package rather than libSBML Core, then getType() will return AST_ORIGINATES_IN_PACKAGE. Callers can then obtain the package-specific type by calling getExtendedType().

See also: getExtendedType()

int libsbmlcs.ASTNode.getTypeCode ( )

int libsbmlcs.ASTBase.getTypeFromName ( string name )

inherited

string libsbmlcs.ASTNode.getUnits ( )

Returns the units of this ASTNode.

SBML Level 3 Version 1 introduced the ability to include an attribute sbml:units on MathML cn elements appearing in SBML mathematical formulas. The value of this attribute can be used to indicate the unit of measurement to be associated with the number in the content of the cn element. The value of this attribute must be the identifier of a unit of measurement defined by SBML or the enclosing Model. Here, the sbml portion is an XML namespace prefix that must be associated with the SBML namespace for SBML Level 3. The following example illustrates how this attribute can be used to define a number with value 10 and unit of measurement second:

<math xmlns="http://www.w3.org/1998/Math/MathML"
      xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
        <cn type="integer" sbml:units="second"> 10 </cn>
</math>

Returns: the units of this ASTNode.

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

See also: SBML_parseL3Formula()

string libsbmlcs.ASTBase.getUnitsPrefix ( )

inherited

SWIGTYPE_p_void libsbmlcs.ASTBase.getUserData ( )

inherited

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.

bool libsbmlcs.ASTBase.hasCnUnits ( )

inherited

bool libsbmlcs.ASTNode.hasCorrectNumberArguments ( )

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

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

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

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

See also: isWellFormedASTNode()

int libsbmlcs.ASTNode.hasTypeAndNumChildren	(	int	type,
		long	numchildren
	)

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

type	the type of ASTNode sought.
numchildren	the number of child nodes sought.

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

bool libsbmlcs.ASTNode.hasUnits ( )

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()

int libsbmlcs.ASTNode.insertChild	(	long	n,
		ASTNode	newChild
	)

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

Parameters

n	long the index of the ASTNode being added
newChild	ASTNode to insert as the nth child

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

*

Warning: Explicitly adding, removing or replacing children of an ASTNode objectmay 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 method ASTNode::isWellFormedASTNode()may also be useful for checking the results of node modifications.

See also: addChild(ASTNode child); prependChild(ASTNode child); replaceChild(long n, ASTNode child); removeChild(long n)

bool libsbmlcs.ASTNode.isAvogadro ( )

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 AST_NAME_AVOGADRO. This method returns true if this node has that type.

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

See also: SBML_parseL3Formula()

bool libsbmlcs.ASTBase.isBinaryFunction ( )

inherited

bool libsbmlcs.ASTNode.isBoolean ( )

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.

bool libsbmlcs.ASTBase.isChild ( )

inherited

bool libsbmlcs.ASTBase.isCiNumber ( )

inherited

bool libsbmlcs.ASTNode.isConstant ( )

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 AST_NAME_AVOGADRO in SBML Level 3.

bool libsbmlcs.ASTBase.isConstantNumber ( )

inherited

bool libsbmlcs.ASTBase.isCSymbolFunction ( )

inherited

bool libsbmlcs.ASTBase.isCSymbolNumber ( )

inherited

bool libsbmlcs.ASTBase.isExponential ( )

inherited

bool libsbmlcs.ASTNode.isFunction ( )

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.

bool libsbmlcs.ASTBase.isFunctionNode ( )

inherited

bool libsbmlcs.ASTNode.isInfinity ( )

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.

bool libsbmlcs.ASTNode.isInteger ( )

Returns true if this node contains an integer value.

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

bool libsbmlcs.ASTNode.isLambda ( )

Returns true if this node is a MathML.

<lambda>.

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

bool libsbmlcs.ASTNode.isLog10 ( )

Returns true if this node represents a log10 function.

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 libsbmlcs.ASTNode.isLogical ( )

Returns true if this node is a MathML logical operator.

The possible MathML logical operators are and, or, not, and xor.

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

bool libsbmlcs.ASTNode.isName ( )

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.

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.

bool libsbmlcs.ASTNode.isNaN ( )

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.

bool libsbmlcs.ASTBase.isNaryFunction ( )

inherited

bool libsbmlcs.ASTNode.isNegInfinity ( )

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.

bool libsbmlcs.ASTNode.isNumber ( )

Returns true if this node contains a number.

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

bool libsbmlcs.ASTBase.isNumberNode ( )

inherited

bool libsbmlcs.ASTNode.isOperator ( )

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.

bool libsbmlcs.ASTNode.isPiecewise ( )

Returns true if this node is the MathML.

<piecewise> construct.

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

bool libsbmlcs.ASTNode.isQualifier ( )

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.

bool libsbmlcs.ASTNode.isRational ( )

Returns true if this node represents a rational number.

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

bool libsbmlcs.ASTNode.isReal ( )

Returns true if this node can represent a real number.

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 libsbmlcs.ASTNode.isRelational ( )

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.

bool libsbmlcs.ASTNode.isSemantics ( )

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

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

bool libsbmlcs.ASTNode.isSetClass ( )

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()

bool libsbmlcs.ASTNode.isSetId ( )

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(); unsetId()

bool libsbmlcs.ASTNode.isSetParentSBMLObject ( )

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 libsbmlcs.ASTNode.isSetStyle ( )

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(); unsetStyle()

bool libsbmlcs.ASTBase.isSetType ( )

inherited

bool libsbmlcs.ASTNode.isSetUnits ( )

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()

bool libsbmlcs.ASTNode.isSetUserData ( )

Returns true if this node has a user data object.

Returns: true if this ASTNode has a user data object set, false otherwise.

bool libsbmlcs.ASTNode.isSqrt ( )

Returns true if this node represents a square root function.

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 libsbmlcs.ASTBase.isTopLevelMathMLFunctionNodeTag ( string name )

inherited

bool libsbmlcs.ASTBase.isTopLevelMathMLNumberNodeTag ( string name )

inherited

bool libsbmlcs.ASTNode.isUMinus ( )

Returns true if this node is a unary minus operator.

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, libsbmlcs.libsbml.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 libsbmlcs.ASTBase.isUnaryFunction ( )

inherited

bool libsbmlcs.ASTNode.isUnknown ( )

Returns true 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 libsbmlcs.ASTNode.isUPlus ( )

Returns true if this node is a unary plus operator.

A node is defined as a unary plus node if it is of type AST_PLUS and has exactly one child.

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

bool libsbmlcs.ASTBase.isUserFunction ( )

inherited

bool libsbmlcs.ASTNode.isWellFormedASTNode ( )

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()

bool libsbmlcs.ASTBase.isWellFormedNode ( )

inherited

void libsbmlcs.ASTBase.loadASTPlugins ( SBMLNamespaces sbmlns )

inherited

void libsbmlcs.ASTBase.logError	(	XMLInputStream	stream,
		XMLToken	element,
		int	code,
		string	msg
	)

inherited

void libsbmlcs.ASTBase.logError	(	XMLInputStream	stream,
		XMLToken	element,
		int	code
	)

inherited

static bool libsbmlcs.ASTNode.operator!=	(	ASTNode	lhs,
		ASTNode	rhs
	)

static

static bool libsbmlcs.ASTNode.operator==	(	ASTNode	lhs,
		ASTNode	rhs
	)

static

int libsbmlcs.ASTNode.prependChild ( ASTNode child )

Adds the given node as a child of this ASTNode.

This method adds child nodes from right to left.

Parameters

child the ASTNode instance to add

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

*

Warning: Explicitly adding, removing or replacing children of an ASTNode objectmay 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 method ASTNode::isWellFormedASTNode()may also be useful for checking the results of node modifications.

See also: addChild(ASTNode child); replaceChild(long n, ASTNode child); insertChild(long n, ASTNode child); removeChild(long n)

bool libsbmlcs.ASTNode.read	(	XMLInputStream	stream,
		string	reqd_prefix
	)

bool libsbmlcs.ASTNode.read ( XMLInputStream stream )

bool libsbmlcs.ASTBase.readAttributes	(	XMLAttributes	attributes,
		SWIGTYPE_p_ExpectedAttributes	expectedAttributes,
		XMLInputStream	stream,
		XMLToken	element
	)

inherited

void libsbmlcs.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 libsbmlcs.ASTNode.removeChild ( long n )

Removes the nth child of this ASTNode object.

Parameters

n	long the index of the child to remove

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

*

Warning: Explicitly adding, removing or replacing children of an ASTNode objectmay 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 method ASTNode::isWellFormedASTNode()may also be useful for checking the results of node modifications.

See also: addChild(ASTNode child); prependChild(ASTNode child); replaceChild(long n, ASTNode child); insertChild(long n, ASTNode child)

void libsbmlcs.ASTNode.renameSIdRefs	(	string	oldid,
		string	newid
	)

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

Parameters

oldid	the old identifier.
newid	the new identifier.

void libsbmlcs.ASTNode.renameUnitSIdRefs	(	string	oldid,
		string	newid
	)

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

oldid	the old identifier.
newid	the new identifier.

void libsbmlcs.ASTNode.replaceArgument	(	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, 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 use as a replacement.

int libsbmlcs.ASTNode.replaceChild	(	long	n,
		ASTNode	newChild
	)

Replaces the nth child of this ASTNode with the given ASTNode.

Parameters

n	long the index of the child to replace
newChild	ASTNode to replace the nth child

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

*

Warning: Explicitly adding, removing or replacing children of an ASTNode objectmay 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 method ASTNode::isWellFormedASTNode()may also be useful for checking the results of node modifications.

See also: addChild(ASTNode child); prependChild(ASTNode child); insertChild(long n, ASTNode child); removeChild(long n)

void libsbmlcs.ASTNode.replaceIDWithFunction	(	string	id,
		ASTNode	function
	)

Replace any nodes of type AST_NAME with the name 'id' from the child 'math' object with the provided ASTNode.

bool libsbmlcs.ASTNode.returnsBoolean ( Model model )

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

model the Model to use as context

See also: isBoolean()

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

bool libsbmlcs.ASTNode.returnsBoolean ( )

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

model the Model to use as context

See also: isBoolean()

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

int libsbmlcs.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 possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.ASTNode.setClass ( string className )

Sets the MathML attribute class of this ASTNode.

Parameters

className string representing the MathML class for this node.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See also: isSetClass(); getClass(); unsetClass()

int libsbmlcs.ASTNode.setDefinitionURL ( XMLAttributes url )

Sets the MathML attribute definitionURL.

Parameters

url	the URL value for the `definitionURL` attribute.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See also: setDefinitionURL(string url); getDefinitionURL(); getDefinitionURLString()

int libsbmlcs.ASTNode.setDefinitionURL ( string url )

Sets the MathML attribute definitionURL.

Parameters

url	the URL value for the `definitionURL` attribute.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

See also: setDefinitionURL(XMLAttributes url); getDefinitionURL(); getDefinitionURLString()

int libsbmlcs.ASTNode.setId ( string id )

Sets the MathML attribute id of this ASTNode.

Parameters

id	`string` representing the identifier.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See also: isSetId(); getId(); unsetId()

void libsbmlcs.ASTBase.setIsChildFlag ( bool flag )

inherited

int libsbmlcs.ASTNode.setName ( string 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 (i.e., ASTNode::isOperator()returns true), number (i.e., ASTNode::isNumber()returns 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 possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.ASTBase.setPackageName ( string name )

inherited

int libsbmlcs.ASTNode.setStyle ( string style )

Sets the MathML attribute style of this ASTNode.

Parameters

style string representing the identifier.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See also: isSetStyle(); getStyle(); unsetStyle()

int libsbmlcs.ASTNode.setType ( int 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 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.

See also: getType(); setType(int Type)

int libsbmlcs.ASTNode.setUnits ( 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

units string representing the unit identifier.

Returns

integer value indicating success/failure of the function. 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.

See also: isSetUnits(); hasUnits()

int libsbmlcs.ASTBase.setUserData ( SWIGTYPE_p_void userData )

inherited

int libsbmlcs.ASTNode.setValue ( int value )

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

As a side effect, this operation 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 possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.ASTNode.setValue	(	int	numerator,
		int	denominator
	)

Sets the value of this ASTNode to the given rational.

As a side effect, this operation sets the node type 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 possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.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 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 possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.ASTNode.setValue	(	double	mantissa,
		int	exponent
	)

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

As a side effet, this operation sets the node type 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 possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.ASTNode.swapChildren ( ASTNode that )

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

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 possible values returned by this function are:

int libsbmlcs.ASTNode.unsetClass ( )

Unsets the MathML class attribute of this ASTNode.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

int libsbmlcs.ASTNode.unsetId ( )

Unsets the MathML id attribute of this ASTNode.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

int libsbmlcs.ASTNode.unsetParentSBMLObject ( )

Unsets the parent SBML object.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

int libsbmlcs.ASTNode.unsetStyle ( )

Unsets the MathML style attribute of this ASTNode.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

int libsbmlcs.ASTNode.unsetUnits ( )

Unsets the units of this ASTNode.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

int libsbmlcs.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 possible values returned by this function are:

void libsbmlcs.ASTNode.write ( XMLOutputStream stream )

void libsbmlcs.ASTNode.writeNodeOfType	(	XMLOutputStream	stream,
		int	type,
		bool	inChildNode
	)

void libsbmlcs.ASTNode.writeNodeOfType	(	XMLOutputStream	stream,
		int	type
	)

Member Data Documentation

bool libsbmlcs.ASTBase.swigCMemOwn

protectedinherited

Detailed Description

The set of possible ASTNode types

Converting between ASTs and text strings

Public Member Functions

Static Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation