ASTNode

java.lang.Object
- org.sbml.jsbml.AbstractTreeNode
- - org.sbml.jsbml.ASTNode

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, TreeNodeWithChangeSupport
```
public class ASTNode
extends AbstractTreeNode
```
A node in the Abstract Syntax Tree (AST) representation of a mathematical expression.

Since:

0.8

Version:

$Rev$

Author:

Andreas Dräger, Nicolas Rodriguez, Alexander Dörr

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class ASTNode.Type
An enumeration of all possible types that can be represented by an abstract syntax tree node.

Nested Classes
Modifier and Type	Class and Description
`static class`	`ASTNode.Type` An enumeration of all possible types that can be represented by an abstract syntax tree node.

Field Summary

Fields
Modifier and Type	Field and Description
`private java.lang.String`	`className`
`private java.lang.String`	`definitionURL` The value of the definitionURL for csymbol element.
`private int`	`denominator`
`private java.lang.String`	`encoding`
`private int`	`exponent`
`private java.lang.String`	`id` Possible attributes for a MathML element
`static java.lang.String`	`IMPLEMENTATION_ASTNODE2` The String representing the facade implementation for the new `ASTNode2` implementation.
`static java.lang.String`	`IMPLEMENTATION_HISTORIC` The String representing the first implementation of the ASTNode, since 0.8.
`static java.lang.String`	`IMPLEMENTATION_VERSION` The String representing the actual implementation of this class, values can be `IMPLEMENTATION_HISTORIC` or `IMPLEMENTATION_ASTNODE2`.
`private static boolean`	`isDebugEnabled`
`private boolean`	`isSetNumberType` Tells if the type attribute of the cn element was set and we need to write it back or if it is set to the default (REAL).
`private java.util.List<ASTNode>`	`listOfNodes` Child nodes.
`private static org.apache.log4j.Logger`	`logger` A `Logger` for this class.
`private double`	`mantissa` The part of a number in scientific format (with an E) that is on the left side of the E (the prefix of the number).
`private java.lang.String`	`name` If no NamedSBase object exists or can be identified when `setName(String)` is called, the given name is stored in this field.
`private int`	`numerator` This value stores the numerator if this.isRational() is `true`, or the value of an integer if this.isInteger() is `true`.
`private MathContainer`	`parentSBMLObject` The container that holds this ASTNode.
`private java.util.SortedMap<java.lang.String,ASTNodePlugin>`	`plugins` `Map` containing the ASTNode plugin object of additional packages with the appropriate name of the package.
`private java.util.List<XMLNode>`	`semanticsAnnotationList` XMLNode that will hold the content of the 'semantics' mathML element.
`private static long`	`serialVersionUID` Generated serial version identifier.
`private java.lang.String`	`style`
`private ASTNode.Type`	`type` The type of this ASTNode.
`private java.lang.String`	`unitId` Since Level 3 SBML allows to equip numbers with unit identifiers.
`static java.lang.String`	`URI_AVOGADRO_DEFINITION` The URI for the definition of the csymbol for avogadro.
`static java.lang.String`	`URI_DELAY_DEFINITION` The URI for the definition of the csymbol for delay.
`static java.lang.String`	`URI_MATHML_DEFINITION` URI for the definition of MathML.
`static java.lang.String`	`URI_MATHML_PREFIX` URI prefix for the definition of MathML, it will be used to write the sbml file
`static java.lang.String`	`URI_RATE_OF_DEFINITION` The URI for the definition of the csymbol for rateOf.
`static java.lang.String`	`URI_TIME_DEFINITION` The URI for the definition of the csymbol for time.
`private CallableSBase`	`variable` A direct pointer to a referenced variable.

Fields inherited from class org.sbml.jsbml.AbstractTreeNode
listOfListeners, parent, resourceBundle

Constructor Summary

Constructors
Constructor and Description
`ASTNode()` Creates a new `ASTNode` of unspecified type and without a pointer to its containing `MathContainer`.
`ASTNode(ASTNode.Type type)` Creates a new `ASTNode` of the given `ASTNode.Type` but without a pointer to its `MathContainer`.
`ASTNode(ASTNode.Type type, MathContainer parent)` Creates and returns a new `ASTNode`.
`ASTNode(ASTNode astNode)` Copy constructor; Creates a deep copy of the given `ASTNode`.
`ASTNode(ASTNode2 node)` Create a new node of type `ASTNode` from the given `ASTNode2`
`ASTNode(CallableSBase nsb)` Creates and returns a new `ASTNode` referring to the given `CallableSBase`.
`ASTNode(CallableSBase nsb, MathContainer parent)` Creates and returns a new `ASTNode` referring to the given `CallableSBase`.
`ASTNode(char operator)` Creates a new `ASTNode` representing an operator, i.e., an internal node.
`ASTNode(char operator, MathContainer parent)` Creates a new `ASTNode` representing an operator, i.e., an internal node.
`ASTNode(double real)` Creates and returns a new `ASTNode`.
`ASTNode(double mantissa, int exponent)` Creates and returns a new `ASTNode`.
`ASTNode(double mantissa, int exponent, MathContainer parent)` Creates and returns a new `ASTNode`.
`ASTNode(double real, MathContainer parent)` Creates and returns a new `ASTNode`.
`ASTNode(int integer)` Creates and returns a new `ASTNode` with the given integer value.
`ASTNode(int integer, MathContainer parent)` Creates and returns a new `ASTNode` with the given integer value for the given `MathContainer` as its parent SBML object.
`ASTNode(int integer, java.lang.String unitsID, MathContainer parent)` Creates and returns a new `ASTNode` with the given integer value with the given associated `unitId` for the given `MathContainer` as its parent SBML object.
`ASTNode(MathContainer parent)` Creates and returns a new `ASTNode`.
`ASTNode(java.lang.String name)` Creates and returns a new `ASTNode` with the given name.
`ASTNode(java.lang.String name, MathContainer parent)` Creates and returns a new `ASTNode` with the given name.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static ASTNode`	`abs(double d, MathContainer parent)` Creates and returns an `ASTNode` that computes the absolute value of the given double value.
`static ASTNode`	`abs(int integer, MathContainer parent)` Creates and returns an `ASTNode` that computes the absolute value of the given integer value.
`void`	`addChild(ASTNode child)` Adds a child to this node.
`void`	`addExtension(java.lang.String nameOrUri, ASTNodePlugin sbasePlugin)` Adds a `ASTNodePlugin` object to this `ASTNode`.
`void`	`addPlugin(java.lang.String nameOrUri, ASTNodePlugin sbasePlugin)` Adds a `ASTNodePlugin` object to this `ASTNode`.
`XMLNode`	`addSemanticsAnnotation(XMLNode semanticsAnnotation)` Adds the given `XMLNode` as a MathML `<semantics>` element to this `ASTNode`.
`private static ASTNode`	`arithmethicOperation(ASTNode.Type operator, ASTNode... ast)` Creates a new `ASTNode` of type `operator` and adds the given nodes as children.
`private void`	`arithmeticOperation(ASTNode.Type operator, ASTNode astnode)` Creates a new node with the type of this node, moves all children of this node to this new node, sets the type of this node to the given operator, adds the new node as left child of this node and the given `ASTNode` as the right child of this node.
`static java.lang.String`	`astNodeToTree(ASTNode n, java.lang.String tree, java.lang.String indent)` Returns a simple tree view of the ASTNode internal, including mainly node type and hierarchy.
`ASTNode`	`clone()`
`ASTNodeValue`	`compile(ASTNodeCompiler compiler)` Compiles this `ASTNode` and returns the result.
`boolean`	`containsUndeclaredUnits()` Returns `true` or `false` depending on whether this `ASTNode` refers to elements such as parameters or numbers with undeclared units.
`ASTNodePlugin`	`createPlugin(java.lang.String nameOrUri)` Creates a new `ASTNodePlugin` for the given package name or URI and adds it to this `ASTNode`.
`UnitDefinition`	`deriveUnit()` Evaluates recursively this ASTNode and creates a new UnitDefinition with respect of all referenced elements.
`static ASTNode`	`diff(ASTNode... ast)` Creates a new `ASTNode` of type MINUS and adds the given nodes as children
`void`	`disablePackage(java.lang.String packageURIOrName)` Disables the given SBML Level 3 package on this `SBMLDocument`.
`ASTNode`	`divideBy(ASTNode ast)` Divides this node by the given node
`ASTNode`	`divideBy(CallableSBase namedSBase)` Divides this node by the given SBML element.
`void`	`enablePackage(java.lang.String packageURIOrName)` Enables the given SBML Level 3 package on this `SBMLDocument`.
`void`	`enablePackage(java.lang.String packageURIOrName, boolean enabled)` Enables or disables the given SBML Level 3 package on this `SBMLDocument`.
`static ASTNode`	`eq(ASTNode left, ASTNode right)` Creates a new `ASTNode` of type RELATIONAL_EQ.
`boolean`	`equals(java.lang.Object object)`
`static ASTNode`	`exp(ASTNode exponent)` Returns a new `ASTNode` that represents Euler's constant raised by the power of the given exponent.
`java.util.List<Parameter>`	`findReferencedGlobalParameters()` Goes through the formula and identifies all global parameters that are referenced by this rate equation.
`static java.lang.String`	`formulaToString(ASTNode tree)` Returns the formula from the given ASTNode as an SBML Level 1 text-string mathematical formula.
`static java.lang.String`	`formulaToString(ASTNode tree, FormulaCompiler compiler)` Returns the formula from the given `ASTNode` as an infix mathematical formula produce by the given `FormulaCompiler`.
`static ASTNode`	`frac(ASTNode numerator, ASTNode denominator)` Creates a new `ASTNode` of type DIVIDE with the given nodes as children.
`static ASTNode`	`frac(int numerator, ASTNode denominator)` Creates a new `ASTNode` that of type DIVIDE with the given numerator and denominator.
`static ASTNode`	`frac(MathContainer container, CallableSBase numerator, CallableSBase denominator)` Creates a new `ASTNode` that divides two `CallableSBase` objects.
`static ASTNode`	`frac(MathContainer container, java.lang.String numeratorId, java.lang.String denominatorId)` Returns a new `ASTNode` that of type DIVIDE with the two entities as numerator and denominator.
`static ASTNode`	`geq(ASTNode left, ASTNode right)` Creates an `ASTNode` representing greater or equal for the two given nodes.
`boolean`	`getAllowsChildren()`
`char`	`getCharacter()` Gets the value of this node as a single character.
`ASTNode`	`getChild(int index)` Gets a child of this node according to an index number.
`javax.swing.tree.TreeNode`	`getChildAt(int i)`
`int`	`getChildCount()`
`java.util.List<ASTNode>`	`getChildren()` Returns the list of children of the current ASTNode.
`java.lang.String`	`getClassName()` Returns the class name of the mathML element represented by this ASTNode.
`java.lang.String`	`getDefinitionURL()` Returns the definitionURL
`int`	`getDenominator()` Gets the value of the denominator of this node.
`java.lang.String`	`getEncoding()` Returns the encoding of the mathML element represented by this ASTNode.
`int`	`getExponent()` Gets the exponent value of this ASTNode.
`ASTNodePlugin`	`getExtension(java.lang.String nameOrUri)` Returns the `ASTNodePlugin` object which matches this package name or URI.
`int`	`getExtensionCount()` Returns the number of `ASTNodePlugin`s of this `ASTNode`.
`java.util.Map<java.lang.String,ASTNodePlugin>`	`getExtensionPackages()` Returns the map containing all the `ASTNodePlugin` extension objects of this `ASTNode`.
`java.lang.String`	`getId()` Returns the id of the mathML element represented by this ASTNode.
`int`	`getInteger()` Gets the value of this node as an integer.
`ASTNode`	`getLeftChild()` Gets the left child of this node.
`java.util.List<ASTNode>`	`getListOfNodes()` Returns the list of children of the current ASTNode.
`java.util.List<ASTNode>`	`getListOfNodes(Filter filter)` Returns the list of children of the current ASTNode that satisfy the given filter.
`java.util.List<XMLNode>`	`getListOfSemanticsAnnotations()` Returns the list of semantics annotations of this node.
`double`	`getMantissa()` Gets the mantissa value of this node.
`java.lang.String`	`getName()` Gets the name of this node.
`int`	`getNumerator()` Gets the value of the numerator of this node.
`int`	`getNumPlugins()` Returns the number of `ASTNodePlugin`s of this `ASTNode`.
`int`	`getNumSemanticsAnnotations()` Gets the number of semantic annotation elements inside this node.
`javax.swing.tree.TreeNode`	`getParent()`
`MathContainer`	`getParentSBMLObject()` This method is convenient when holding an object nested inside other objects in an SBML model.
`ASTNodePlugin`	`getPlugin(java.lang.String nameOrUri)` Returns an `ASTNodePlugin` for an SBML Level 3 package extension with the given package name or URI.
`double`	`getReal()` Gets the real-numbered value of this node.
`java.util.Set<NamedSBase>`	`getReferencedNamedSBases()` Returns a set of all the `NamedSBase` referenced on this node and all his descendant.
`ASTNode`	`getRightChild()` Returns the last child in the list of children of this node.
`XMLNode`	`getSemanticsAnnotation(int n)` Gets the nth `<semantics>` annotation of this node.
`java.lang.String`	`getStyle()` Returns the style of the mathML element represented by this ASTNode.
`ASTNode.Type`	`getType()` Returns the type of this node.
`java.lang.String`	`getUnits()` Returns the units attribute.
`UnitDefinition`	`getUnitsInstance()` Creates or obtains a `UnitDefinition` corresponding to the unit that has been set for this `ASTNode` and returns a pointer to it.
`CallableSBase`	`getVariable()` Returns the variable of this node.
`static ASTNode`	`gt(ASTNode left, ASTNode right)` Creates an `ASTNode` representing greater than for the two given left and right child.
`int`	`hashCode()`
`boolean`	`hasUnits()` Returns `true` if the current ASTNode or any of his descendant has a unit defined.
`private void`	`initDefaults()` Initializes the default values/attributes of the node.
`void`	`insertChild(int n, ASTNode newChild)` Inserts the given `ASTNode` at point n in the list of children of this `ASTNode`.
`boolean`	`isBoolean()` Returns `true` if this node has a boolean type (a logical operator, a relational operator, or the constants `true` or `false`).
`boolean`	`isConstant()` Returns `true` if this node represents a MathML constant (e.g., `true`, Pi).
`boolean`	`isDifference()` Checks if this `ASTNode` represents a difference.
`boolean`	`isExtendedByOtherPackages()` Returns `true` if this object is extended by other packages.
`boolean`	`isFunction()` Returns `true` if this node represents a function.
`boolean`	`isInfinity()` Returns `true` if this node represents the special IEEE 754 value infinity, `false` otherwise.
`boolean`	`isInteger()` Returns `true` if this node contains an integer value, `false` otherwise.
`boolean`	`isLambda()` Returns `true` if this node is a MathML <lambda>, `false` otherwise.
`boolean`	`isLiteral()` Returns `true` if this node is constant or of type INTEGER, REAL or RATIONAL, `false` otherwise.
`boolean`	`isLog10()` Returns `true` if this node represents a log10() function, `false` otherwise.
`boolean`	`isLogical()` Returns `true` if this node is a MathML logical operator (i.e., and, or, not, xor).
`boolean`	`isMinusOne()` Returns `true` if this astnode represents the number minus one (either as integer or as real value).
`boolean`	`isName()` Returns `true` if this node is a user-defined `Variable` name in SBML L1, L2 (MathML), or the special symbols time, Avogadro or rateOf.
`boolean`	`isNaN()` Returns `true` if this node is a type Real and represents the special IEEE 754 value 'not a number' `Double.NaN`, `false` otherwise.
`boolean`	`isNegInfinity()` Returns `true` if this node represents the special IEEE 754 value 'negative infinity' `Double.NEGATIVE_INFINITY`, `false` otherwise.
`boolean`	`isNumber()` Returns `true` if this node contains a number, `false` otherwise.
`boolean`	`isOne()` Returns `true` if this `ASTNode` represents the number one (either as integer or as real value).
`boolean`	`isOperator()` Returns `true` if this node is a mathematical operator, meaning, +, -, *, / or ^ (power).
`boolean`	`isPackageEnabled(java.lang.String packageURIOrName)` Returns `true` if the given SBML Level 3 package is enabled within the containing `SBMLDocument`.
`boolean`	`isPackageURIEnabled(java.lang.String packageURIOrName)` Returns `true` if the given SBML Level 3 package is enabled within the containing `SBMLDocument`.
`boolean`	`isPiecewise()` Returns `true` if this node is the MathML <piecewise> construct, `false` otherwise.
`boolean`	`isRational()` Returns `true` if this node represents a rational number, `false` otherwise.
`boolean`	`isReal()` Returns `true` if this node can represent a real number, `false` otherwise.
`boolean`	`isRelational()` Returns `true` if this node is a MathML relational operator, meaning ==, >=, >, <, <=, and !=.
`boolean`	`isSemantics()` Return true if this node contain some semantics annotations.
`boolean`	`isSetClassName()`
`boolean`	`isSetDefinitionURL()`
`boolean`	`isSetEncoding()`
`boolean`	`isSetId()`
`boolean`	`isSetName()`
`boolean`	`isSetNumberType()` Returns `true` if the number type is set.
`boolean`	`isSetParentSBMLObject()` Checks if a parent SBML object, i.e., a `MathContainer`, is set as a parent SBML object for this `ASTNode`.
`boolean`	`isSetPlugin(java.lang.String nameOrUri)` Returns `true` if an `ASTNodePlugin` is defined for the given package.
`boolean`	`isSetStyle()`
`boolean`	`isSetUnits()` Returns `true` if a unit is defined on this node.
`boolean`	`isSqrt()` Returns `true` if this node represents a square root function, `false` otherwise.
`boolean`	`isString()` Returns `true` if this node is a name or refers to a `FunctionDefinition`.
`boolean`	`isSum()` Checks if this `ASTNode` represents a sum.
`boolean`	`isUMinus()` Returns `true` if this node is a unary minus operator, `false` otherwise.
`boolean`	`isUnary()` Checks whether the number of child nodes is exactly one.
`boolean`	`isUnknown()` Returns `true` if this node has an `ASTNode.Type.UNKNOWN` type.
`boolean`	`isVariable()` Returns `true` if this node represents a `Variable`.
`boolean`	`isVector()` Checks if this `ASTNode` represents a vector.
`boolean`	`isZero()` Returns `true` if this node represents the number zero (either as integer or as real value).
`static ASTNode`	`leq(ASTNode left, ASTNode right)` Creates an `ASTNode` representing less or equal for the two given left and right child.
`static ASTNode`	`log(ASTNode value)` Creates an `ASTNode` representing a logarithm to base 10 of the given value.
`static ASTNode`	`log(ASTNode base, ASTNode value)` Creates an `ASTNode` that represents the logarithm function with the given base and value.
`static ASTNode`	`lt(ASTNode left, ASTNode right)` Creates an `ASTNode` that performs a less than comparison between two `ASTNode`s.
`static ASTNode`	`lt(java.lang.String variable, ASTNode node)` Creates an `ASTNode` that performs a less than comparison between a variable and another `ASTNode`.
`ASTNode`	`minus(ASTNode ast)` Subtracts the given ASTNode from this node.
`ASTNode`	`minus(double real)` Subtracts the given number from this node.
`ASTNode`	`minus(int integer)` Subtracts the given integer from this node.
`ASTNode`	`minus(int integer, java.lang.String unitsID)`
`ASTNode`	`multiplyWith(ASTNode... nodes)` Multiplies this `ASTNode` with the given nodes, i.e., all given nodes will be children of this node, whose type will be set to `ASTNode.Type.TIMES`.
`ASTNode`	`multiplyWith(ASTNode ast)` Multiplies this `ASTNode` with the given node
`ASTNode`	`multiplyWith(CallableSBase nsb)` Multiplies this `ASTNode` with the given SBML element.
`static ASTNode`	`neq(ASTNode left, ASTNode right)` Creates an `ASTNode` that performs a not equal comparison between two `ASTNode`s.
`static ASTNode`	`parseFormula(java.lang.String formula)` Parses a text-string mathematical formula and returns a representation as an Abstract Syntax Tree.
`static ASTNode`	`parseFormula(java.lang.String formula, IFormulaParser parser)` Parses a text-string mathematical formula, using the given `IFormulaParser` and returns a representation as an Abstract Syntax Tree.
`static ASTNode`	`parseMathML(java.lang.String mathML)`
`static ASTNode`	`piecewise(ASTNode node, ASTNode... nodes)` Creates a piecewise `ASTNode`.
`static ASTNode`	`piecewise(MathContainer parentSBMLObject, ASTNode[] nodes)`
`ASTNode`	`plus(ASTNode ast)` Adds a given node to this node.
`ASTNode`	`plus(CallableSBase nsb)` Adds an SBML element to this node.
`ASTNode`	`plus(double real)` Adds a number to this node.
`ASTNode`	`plus(int integer)` Adds an integer number to this node.
`static ASTNode`	`pow(ASTNode basis, ASTNode exponent)` Creates a power `ASTNode`.
`static ASTNode`	`pow(ASTNode basis, double exponent)` Creates a power `ASTNode`.
`static ASTNode`	`pow(ASTNode basis, int exponent)` Creates a power `ASTNode`.
`static ASTNode`	`pow(MathContainer container, CallableSBase basis, CallableSBase exponent)` Raises the given basis by the power of the given exponent.
`void`	`prependChild(ASTNode child)` Adds the given node as a child of this ASTNode.
`java.lang.String`	`printASTNode()` Returns the infix formula representing this ASTNode or an empty String if there was a problem to construct the formula.
`ASTNode`	`raiseByThePowerOf(ASTNode exponent)` Raises this ASTNode by the power of the value of the given node.
`ASTNode`	`raiseByThePowerOf(CallableSBase nsb)` Raises this ASTNode by the power of the value of this named SBase object.
`ASTNode`	`raiseByThePowerOf(double exponent)` Raises this `ASTNode` by the power of the given number.
`static ASTNode`	`readMathMLFromString(java.lang.String xml)` Reads the MathML from the given XML string.
`private void`	`reduceToBinary()` Reduces this `ASTNode` to a binary tree, e.g., if the formula in this `ASTNode` is and(x, y, z) then the formula of the reduced node would be and(and(x, y), z).
`boolean`	`refersTo(java.lang.String id)` Returns `true` if this node or one of its descendants contains some identifier with the given id.
`private static ASTNode`	`relational(ASTNode.Type type, ASTNode left, ASTNode right)` Creates a relational `ASTNode` of the given type with the two given children left and right.
`boolean`	`removeChild(int n)` Removes child n of this ASTNode.
`void`	`replaceArgument(java.lang.String bvar, ASTNode arg)` Replaces occurrences of a name within this ASTNode with the name/value/formula represented by the second argument ASTNode, e.g., if the formula in this ASTNode is x + y; bvar is x and arg is an ASTNode representing the real value 3 ReplaceArgument substitutes 3 for x within this ASTNode.
`ASTNode`	`replaceChild(int n, ASTNode newChild)` Replaces the n^th child of this ASTNode with the given ASTNode.
`private void`	`resetParentSBMLObject(ASTNode node)` Resets the parentSBMLObject to null recursively.
`static ASTNode`	`root(ASTNode rootExponent, ASTNode radicand)` Creates a root `ASTNode`.
`void`	`setCharacter(char value)` Sets the value of this ASTNode to the given character.
`void`	`setClassName(java.lang.String className)` Sets the class name of the mathML element represented by this ASTNode.
`void`	`setDefinitionURL(java.lang.String definitionURL)`
`void`	`setEncoding(java.lang.String encoding)` Sets the encoding of the mathML element represented by this ASTNode.
`void`	`setId(java.lang.String id)` Sets the id of the mathML element represented by this ASTNode.
`void`	`setIsSetNumberType(boolean isSetNumberType)`
`void`	`setName(java.lang.String name)` Sets the value of this `ASTNode` to the given name.
`(package private) static void`	`setParentSBMLObject(ASTNode node, MathContainer parent)` Sets the Parent of the node and its children to the given value
`private static void`	`setParentSBMLObject(ASTNode node, MathContainer parent, int depth)` Sets the parent of the node and its children to the given value
`void`	`setParentSBMLObject(MathContainer parent)` Sets the Parent of the node to the given value
`void`	`setStyle(java.lang.String style)` Sets the style of the mathML element represented by this `ASTNode`.
`void`	`setType(ASTNode.Type type)` Sets the type of this ASTNode to the given Type.
`void`	`setType(java.lang.String typeStr)` Sets the type from a String.
`void`	`setUnits(java.lang.String unitId)` Sets the units attribute.
`void`	`setUnits(Unit.Kind unit)`
`void`	`setUnits(UnitDefinition ud)`
`void`	`setValue(double value)` Sets the value of this ASTNode to the given double number and sets the node type to REAL.
`void`	`setValue(double mantissa, int exponent)` Sets the value of this ASTNode to the given real (double) in two parts: the mantissa and the exponent.
`void`	`setValue(int value)` Sets the value of this ASTNode to the given (long) integer and sets the node type to INTEGER.
`void`	`setValue(int numerator, int denominator)` Sets the value of this ASTNode to the given rational in two parts: the numerator and denominator.
`void`	`setVariable(CallableSBase variable)` Allows you to directly set an instance of `CallableSBase` as the variable of this `ASTNode`.
`ASTNode`	`sqrt()` Applies the square root function on this syntax tree and returns the resulting tree.
`static ASTNode`	`sqrt(ASTNode radicand)` Creates a root `ASTNode`.
`static ASTNode`	`sum(ASTNode... ast)` Creates a new `ASTNode` of type Plus with the given nodes as children.
`static ASTNode`	`sum(MathContainer parent, CallableSBase... sbase)` Sum of several NamedSBase objects.
`void`	`swapChildren(ASTNode that)` Swaps the children of this `ASTNode` with the children of that `ASTNode`.
`static ASTNode`	`times(ASTNode... ast)` Creates an `ASTNode` of type times and adds the given nodes as children.
`static ASTNode`	`times(MathContainer parent, CallableSBase... sbase)` Multiplies several `CallableSBase` objects.
`ASTNode2`	`toASTNode2()` Return the `ASTNode2` corresponding to the current `ASTNode`
`java.lang.String`	`toFormula()` Converts this `ASTNode` to a text string using a specific syntax for mathematical formulas.
`java.lang.String`	`toFormula(FormulaCompiler compiler)` Converts this `ASTNode` to a text string using a specific `FormulaCompiler`.
`java.lang.String`	`toLaTeX()` Converts this node recursively into a LaTeX formatted String.
`java.lang.String`	`toMathML()` Converts this node recursively into a MathML string that corresponds to the subset of MathML defined in the SBML specification.
`java.lang.String`	`toSimpleString()` Returns a simple String representing the content of the ASTNode.
`java.lang.String`	`toString()`
`static ASTNode`	`uMinus(ASTNode ast)` Creates a new `ASTNode` that has exactly one child and which is of type minus, i.e., this negates what is encoded in ast.
`static ASTNode`	`uMinus(MathContainer container, CallableSBase sbase)` Creates a new `ASTNode` that has exactly one child and which is of type minus, i.e., this negates what is encoded in ast.
`void`	`unsetExtension(java.lang.String nameOrUri)` Unsets the `ASTNodePlugin` extension object which matches this package name or URI.
`void`	`unsetPlugin(java.lang.String nameOrUri)` Unsets the `ASTNodePlugin` plugin object which matches this package name or URI.
`void`	`unsetUnits()` Unset the units attribute.
`void`	`updateVariables()` For a better performance `ASTNode`s can store a direct pointer to a variable element.

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Generated serial version identifier.
    
    See Also:
    
    Constant Field Values
  - URI_AVOGADRO_DEFINITION
```
public static final transient java.lang.String URI_AVOGADRO_DEFINITION
```
    The URI for the definition of the csymbol for avogadro.
    
    See Also:
    
    Constant Field Values
  - URI_DELAY_DEFINITION
```
public static final transient java.lang.String URI_DELAY_DEFINITION
```
    The URI for the definition of the csymbol for delay.
    
    See Also:
    
    Constant Field Values
  - URI_MATHML_DEFINITION
```
public static final transient java.lang.String URI_MATHML_DEFINITION
```
    URI for the definition of MathML.
    
    See Also:
    
    Constant Field Values
  - URI_MATHML_PREFIX
```
public static final java.lang.String URI_MATHML_PREFIX
```
    URI prefix for the definition of MathML, it will be used to write the sbml file
    
    See Also:
    
    Constant Field Values
  - URI_RATE_OF_DEFINITION
```
public static final transient java.lang.String URI_RATE_OF_DEFINITION
```
    The URI for the definition of the csymbol for rateOf.
    
    See Also:
    
    Constant Field Values
  - URI_TIME_DEFINITION
```
public static final transient java.lang.String URI_TIME_DEFINITION
```
    The URI for the definition of the csymbol for time.
    
    See Also:
    
    Constant Field Values
  - IMPLEMENTATION_HISTORIC
```
public static final java.lang.String IMPLEMENTATION_HISTORIC
```
    The String representing the first implementation of the ASTNode, since 0.8.
    
    See Also:
    
    Constant Field Values
  - IMPLEMENTATION_ASTNODE2
```
public static final java.lang.String IMPLEMENTATION_ASTNODE2
```
    The String representing the facade implementation for the new ASTNode2 implementation.
    
    See Also:
    
    Constant Field Values
  - IMPLEMENTATION_VERSION
```
public static final java.lang.String IMPLEMENTATION_VERSION
```
    The String representing the actual implementation of this class, values can be IMPLEMENTATION_HISTORIC or IMPLEMENTATION_ASTNODE2.
    
    See Also:
    
    Constant Field Values
  - definitionURL
```
private java.lang.String definitionURL
```
    The value of the definitionURL for csymbol element. Level 3 extensions can create new csymbol element that we would not necessary be aware of, so we need to store the attribute value.
  - denominator
```
private int denominator
```
  - exponent
```
private int exponent
```
  - id
```
private java.lang.String id
```
    Possible attributes for a MathML element
  - style
```
private java.lang.String style
```
  - className
```
private java.lang.String className
```
  - encoding
```
private java.lang.String encoding
```
  - semanticsAnnotationList
```
private java.util.List<XMLNode> semanticsAnnotationList
```
    XMLNode that will hold the content of the 'semantics' mathML element.
  - isSetNumberType
```
private boolean isSetNumberType
```
    Tells if the type attribute of the cn element was set and we need to write it back or if it is set to the default (REAL).
  - listOfNodes
```
private java.util.List<ASTNode> listOfNodes
```
    Child nodes.
  - logger
```
private static final transient org.apache.log4j.Logger logger
```
    A Logger for this class.
  - isDebugEnabled
```
private static final transient boolean isDebugEnabled
```
  - mantissa
```
private double mantissa
```
    The part of a number in scientific format (with an E) that is on the left side of the E (the prefix of the number). For instance, in the number 3.5E-2.7 the mantissa is 3.5.
  - name
```
private java.lang.String name
```
    If no NamedSBase object exists or can be identified when setName(String) is called, the given name is stored in this field.
  - numerator
```
private int numerator
```
    This value stores the numerator if this.isRational() is true, or the value of an integer if this.isInteger() is true.
  - parentSBMLObject
```
private MathContainer parentSBMLObject
```
    The container that holds this ASTNode.
  - type
```
private ASTNode.Type type
```
    The type of this ASTNode.
  - unitId
```
private java.lang.String unitId
```
    Since Level 3 SBML allows to equip numbers with unit identifiers. In this case a reference to an identifier of a UnitDefinition in the model can be stored here.
  - variable
```
private CallableSBase variable
```
    A direct pointer to a referenced variable. This can save a lot of computation time because it will then not be necessary to query the corresponding model again and again for this variable.
  - plugins
```
private java.util.SortedMap<java.lang.String,ASTNodePlugin> plugins
```
    Map containing the ASTNode plugin object of additional packages with the appropriate name of the package.
- Constructor Detail
  - ASTNode
```
public ASTNode()
```
    Creates a new ASTNode of unspecified type and without a pointer to its containing MathContainer.
  - ASTNode
```
public ASTNode(ASTNode astNode)
```
    Copy constructor; Creates a deep copy of the given ASTNode.
    
    Parameters:
    
    astNode - the ASTNode to be copied.
  - ASTNode
```
public ASTNode(CallableSBase nsb)
```
    Creates and returns a new ASTNode referring to the given CallableSBase.
    
    Parameters:
    
    nsb -
  - ASTNode
```
public ASTNode(ASTNode2 node)
```
    Create a new node of type ASTNode from the given ASTNode2
    
    Parameters:
    
    node - ASTNode2
  - ASTNode
```
public ASTNode(CallableSBase nsb,
               MathContainer parent)
```
    Creates and returns a new ASTNode referring to the given CallableSBase.
    
    Parameters:
    
    nsb -
    
    parent -
  - ASTNode
```
public ASTNode(char operator)
```
    Creates a new ASTNode representing an operator, i.e., an internal node.
    
    Parameters:
    
    operator -
  - ASTNode
```
public ASTNode(char operator,
               MathContainer parent)
```
    Creates a new ASTNode representing an operator, i.e., an internal node.
    
    Parameters:
    
    operator -
    
    parent -
  - ASTNode
```
public ASTNode(double real)
```
    Creates and returns a new ASTNode.
    
    Parameters:
    
    real -
  - ASTNode
```
public ASTNode(double mantissa,
               int exponent)
```
    Creates and returns a new ASTNode.
    
    Parameters:
    
    mantissa -
    
    exponent -
  - ASTNode
```
public ASTNode(double mantissa,
               int exponent,
               MathContainer parent)
```
    Creates and returns a new ASTNode.
    
    Parameters:
    
    mantissa -
    
    exponent -
    
    parent -
  - ASTNode
```
public ASTNode(double real,
               MathContainer parent)
```
    Creates and returns a new ASTNode.
    
    Parameters:
    
    real -
    
    parent -
  - ASTNode
```
public ASTNode(int integer)
```
    Creates and returns a new ASTNode with the given integer value.
    
    Parameters:
    
    integer -
  - ASTNode
```
public ASTNode(int integer,
               MathContainer parent)
```
    Creates and returns a new ASTNode with the given integer value for the given MathContainer as its parent SBML object.
    
    Parameters:
    
    integer -
    
    parent -
  - ASTNode
```
public ASTNode(int integer,
               java.lang.String unitsID,
               MathContainer parent)
```
    Creates and returns a new ASTNode with the given integer value with the given associated unitId for the given MathContainer as its parent SBML object.
    
    Parameters:
    
    integer -
    
    unitsID -
    
    parent -
  - ASTNode
```
public ASTNode(MathContainer parent)
```
    Creates and returns a new ASTNode. By default, the returned node will have a type of ASTNode.Type.UNKNOWN. The calling code should set the node type to something else as soon as possible using setType(int)
    
    Parameters:
    
    parent - the parent SBML object
  - ASTNode
```
public ASTNode(java.lang.String name)
```
    Creates and returns a new ASTNode with the given name.
    
    Parameters:
    
    name - the name of this ASTNode
  - ASTNode
```
public ASTNode(java.lang.String name,
               MathContainer parent)
```
    Creates and returns a new ASTNode with the given name.
    
    Parameters:
    
    name - the name of this ASTNode
    
    parent - the parent SBML object.
  - ASTNode
```
public ASTNode(ASTNode.Type type)
```
    Creates a new ASTNode of the given ASTNode.Type but without a pointer to its MathContainer.
    
    Parameters:
    
    type -
  - ASTNode
```
public ASTNode(ASTNode.Type type,
               MathContainer parent)
```
    Creates and returns a new ASTNode.
    
    Parameters:
    
    type - the type of the ASTNode to create.
    
    parent - the parent SBML object.
- Method Detail
  - abs
```
public static ASTNode abs(double d,
                          MathContainer parent)
```
    Creates and returns an ASTNode that computes the absolute value of the given double value.
    
    Parameters:
    
    d - a double value
    
    parent - the parent ASTNode
    
    Returns:
    
    an ASTNode that computes the absolute value of the given double value.
  - abs
```
public static ASTNode abs(int integer,
                          MathContainer parent)
```
    Creates and returns an ASTNode that computes the absolute value of the given integer value.
    
    Parameters:
    
    integer - an integer value
    
    parent - the parent ASTNode
    
    Returns:
    
    an ASTNode that computes the absolute value of the given integer value.
  - arithmethicOperation
```
private static ASTNode arithmethicOperation(ASTNode.Type operator,
                                            ASTNode... ast)
```
    Creates a new ASTNode of type operator and adds the given nodes as children.
    
    Parameters:
    
    operator - the type of arithmetic operation
    
    ast - the children of the new ASTNode
    
    Returns:
    
    a new ASTNode of type operator and adds the given nodes as children.
  - diff
```
public static ASTNode diff(ASTNode... ast)
```
    Creates a new ASTNode of type MINUS and adds the given nodes as children
    
    Parameters:
    
    ast - the children of the new ASTNode
    
    Returns:
    
    a new ASTNode of type MINUS and adds the given nodes as children
  - eq
```
public static ASTNode eq(ASTNode left,
                         ASTNode right)
```
    Creates a new ASTNode of type RELATIONAL_EQ.
    
    Parameters:
    
    left - the left child.
    
    right - the right child.
    
    Returns:
    
    a new ASTNode of type RELATIONAL_EQ.
  - exp
```
public static ASTNode exp(ASTNode exponent)
```
    Returns a new ASTNode that represents Euler's constant raised by the power of the given exponent.
    
    Parameters:
    
    exponent - the exponent
    
    Returns:
    
    a new ASTNode that represents Euler's constant raised by the power of the given exponent.
  - formulaToString
```
public static java.lang.String formulaToString(ASTNode tree)
                                        throws SBMLException
```
    Returns the formula from the given ASTNode as an SBML Level 1 text-string mathematical formula.
    
    Parameters:
    
    tree - the root of the ASTNode formula expression tree
    
    Returns:
    
    the formula from the given AST as an SBML Level 1 text-string mathematical formula. The caller owns the returned string and is responsible for freeing it when it is no longer needed. null is returned if the given argument is null.
    
    Throws:
    
    SBMLException - if the ASTNode is not well formed.
    
    See Also:
    
    toFormula()
  - formulaToString
```
public static java.lang.String formulaToString(ASTNode tree,
                                               FormulaCompiler compiler)
                                        throws SBMLException
```
    Returns the formula from the given ASTNode as an infix mathematical formula produce by the given FormulaCompiler.
    
    Parameters:
    
    tree - the root of the ASTNode formula expression tree
    
    compiler - the FormulaCompiler to use
    
    Returns:
    
    the formula from the given AST as an infix mathematical formula. null is returned if one of the given arguments is null.
    
    Throws:
    
    SBMLException - if the ASTNode is not well formed.
    
    See Also:
    
    toFormula(), FormulaCompiler, FormulaCompilerLibSBML
  - frac
```
public static ASTNode frac(ASTNode numerator,
                           ASTNode denominator)
```
    Creates a new ASTNode of type DIVIDE with the given nodes as children.
    
    Parameters:
    
    numerator - the numerator
    
    denominator - the denominator
    
    Returns:
    
    a new ASTNode of type DIVIDE with the given nodes as children.
  - frac
```
public static ASTNode frac(int numerator,
                           ASTNode denominator)
```
    Creates a new ASTNode that of type DIVIDE with the given numerator and denominator.
    
    Parameters:
    
    numerator - the numerator
    
    denominator - the denominator
    
    Returns:
    
    a new ASTNode that of type DIVIDE with the given numerator and denominator.
  - frac
```
public static ASTNode frac(MathContainer container,
                           CallableSBase numerator,
                           CallableSBase denominator)
```
    Creates a new ASTNode that divides two CallableSBase objects.
    
    Parameters:
    
    container - the parent object
    
    numerator - the numerator
    
    denominator - the denominator
    
    Returns:
    
    a new ASTNode that divides two CallableSBase objects.
  - frac
```
public static ASTNode frac(MathContainer container,
                           java.lang.String numeratorId,
                           java.lang.String denominatorId)
```
    Returns a new ASTNode that of type DIVIDE with the two entities as numerator and denominator.
    
    Parameters:
    
    container - the parent object
    
    numeratorId - the numerator
    
    denominatorId - the numerator
    
    Returns:
    
    a new ASTNode that of type DIVIDE with the two entities as numerator and denominator.
  - geq
```
public static ASTNode geq(ASTNode left,
                          ASTNode right)
```
    Creates an ASTNode representing greater or equal for the two given nodes.
    
    Parameters:
    
    left - the left child.
    
    right - the right child.
    
    Returns:
    
    an ASTNode representing greater or equal.
  - gt
```
public static ASTNode gt(ASTNode left,
                         ASTNode right)
```
    Creates an ASTNode representing greater than for the two given left and right child.
    
    Parameters:
    
    left - the left child.
    
    right - the right child.
    
    Returns:
    
    an ASTNode representing greater than for the two given left and right child.
  - leq
```
public static ASTNode leq(ASTNode left,
                          ASTNode right)
```
    Creates an ASTNode representing less or equal for the two given left and right child.
    
    Parameters:
    
    left - the left child.
    
    right - the right child.
    
    Returns:
    
    an ASTNode representing less or equal for the two given left and right child.
  - log
```
public static ASTNode log(ASTNode value)
```
    Creates an ASTNode representing a logarithm to base 10 of the given value.
    
    Parameters:
    
    value - the value which is the argument of the logarithm.
    
    Returns:
    
    an ASTNode representing a logarithm to base 10 of the given value.
  - log
```
public static ASTNode log(ASTNode base,
                          ASTNode value)
```
    Creates an ASTNode that represents the logarithm function with the given base and value. The parent SBML object will be taken from the ASTNode value.
    
    Parameters:
    
    base - The basis of this logarithm. Can be null; then a base of 10 will be assumed.
    
    value - Must not be null.
    
    Returns:
    
    An ASTNode representing the logarithm of the given value with respect to the given base or to the base 10 if base is null.
  - lt
```
public static ASTNode lt(ASTNode left,
                         ASTNode right)
```
    Creates an ASTNode that performs a less than comparison between two ASTNodes. The parent SBML object of the resulting node will be taken from the left node.
    
    Parameters:
    
    left - the left child.
    
    right - the right child.
    
    Returns:
    
    an ASTNode that performs a less than comparison between two ASTNodes.
  - lt
```
public static ASTNode lt(java.lang.String variable,
                         ASTNode node)
```
    Creates an ASTNode that performs a less than comparison between a variable and another ASTNode. The parent SBML object will be taken from the given ASTNode.
    
    Parameters:
    
    variable - the left child.
    
    node - the right child.
    
    Returns:
    
    an ASTNode that performs a less than comparison between a variable and another ASTNode.
  - neq
```
public static ASTNode neq(ASTNode left,
                          ASTNode right)
```
    Creates an ASTNode that performs a not equal comparison between two ASTNodes.
    
    Parameters:
    
    left - the left child.
    
    right - the right child.
    
    Returns:
    
    an ASTNode that performs a not equal comparison between two ASTNodes.
  - parseFormula
```
public static ASTNode parseFormula(java.lang.String formula)
                            throws ParseException
```
    Parses a text-string mathematical formula and returns a representation as an Abstract Syntax Tree.
    Support the syntax defined in FormulaParserLL3 which is almost the same syntax as defined in the LibSBML L3 parser. The things not supported for now are the units associated with numbers.
    Parsing of the various MathML functions and constants are all case-sensitive by default: names such as Cos and COS are not parsed as the MathML cosine operator, <cos>. As well, if you have an SBML entities (species, parameter, ...) that has an id identical to one of the supported mathML element, the parser will interpret the String as the mathML element and not the SBML entity.
    You can change this behaviour by using the FormulaParserLL3.setCaseSensitive(boolean) method and using the parseFormula(String, IFormulaParser) method instead of this one:
    FormulaParserLL3 caseSensitiveParser = new FormulaParserLL3(new StringReader("")); caseInsensitiveParser.setCaseSensitive(false); ASTNode n = ASTNode.parseFormula("Cos(x)", caseInsensitiveParser);
    This method has a different behaviour since JSBML-1.0 compare to JSBML-0.8. There is a different operator precedence, the parsing is now case sensitive for mathML elements and boolean operators are now differently interpreted: '&&' and '||' are used instead of 'and' and 'or'.
    If you want to use the parser used in JSBML-0.8, you can do that by using the FormulaParser parser class and using the parseFormula(String, IFormulaParser) method instead of this one:
    FormulaParser oldParser = new FormulaParser(new StringReader("")); ASTNode n = ASTNode.parseFormula("x and y", oldParser);
    If you are not satisfied with the behavior of the existing parsers, you can create your own, you just need to implement the IFormulaParser interface.
    Parameters:
    
    formula - a text-string mathematical formula.
    
    Returns:
    
    an ASTNode representing the formula.
    
    Throws:
    
    ParseException - If the given formula is not of valid format or cannot be parsed for other reasons.
    
    See Also:
    
    parseFormula(String, IFormulaParser), FormulaParserLL3, FormulaParser
  - parseFormula
```
public static ASTNode parseFormula(java.lang.String formula,
                                   IFormulaParser parser)
                            throws ParseException
```
    Parses a text-string mathematical formula, using the given IFormulaParser and returns a representation as an Abstract Syntax Tree.
    Support the syntax defined in the IFormulaParser provided.
    You can for example use you own parser or use an existing parser with different options.
    For example, you can change the behaviour of the FormulaParserLL3 class by using the FormulaParserLL3.setCaseSensitive(boolean) method:
    FormulaParserLL3 caseSensitiveParser = new FormulaParserLL3(new StringReader("")); caseInsensitiveParser.setCaseSensitive(false); ASTNode n = ASTNode.parseFormula("Cos(x)", caseInsensitiveParser);
    You can as well use the FormulaParser class to get the same parsing behaviour as in JSBML-0.8:
    FormulaParser oldParser = new FormulaParser(new StringReader("")); ASTNode n = ASTNode.parseFormula("x and y", oldParser);
    If you are not satisfied with the behaviour of the existing parsers, you can create your own, you just need to implement the IFormulaParser interface.
    Parameters:
    
    formula - a text-string mathematical formula.
    
    parser - a formula parser.
    
    Returns:
    
    an ASTNode representing the formula.
    
    Throws:
    
    ParseException - If the given formula is not of valid format or cannot be parsed for other reasons.
    
    See Also:
    
    parseFormula(String), FormulaParserLL3, FormulaParser
  - parseMathML
```
public static ASTNode parseMathML(java.lang.String mathML)
```
    Parameters:
    
    mathML - a String in MathML format.
    
    Returns:
    
    An ASTNode representation of the given MathML String.
    
    See Also:
    
    readMathMLFromString(String)
  - piecewise
```
public static ASTNode piecewise(ASTNode node,
                                ASTNode... nodes)
```
    Creates a piecewise ASTNode.
    At least one ASTNode must be given as a child. The parent SBML object of this first node will be the parent of the resulting ASTNode.
    
    Parameters:
    
    node - the parent SBML object of this node will be the parent of the resulting ASTNode.
    
    nodes - the children of the new piecewise ASTNode
    
    Returns:
    
    a piecewise ASTNode.
  - piecewise
```
public static ASTNode piecewise(MathContainer parentSBMLObject,
                                ASTNode[] nodes)
```
    Parameters:
    
    parentSBMLObject - a link to the container in which this ASTNode will be inserted. This can be useful if complex operations on units, species, etc. are necessary when creating this formula. Can be null.
    
    nodes -
    
    Returns:
    
    See Also:
    
    piecewise(ASTNode, ASTNode...)
  - pow
```
public static ASTNode pow(ASTNode basis,
                          ASTNode exponent)
```
    Creates a power ASTNode.
    
    Parameters:
    
    basis - the basis
    
    exponent - the exponent
    
    Returns:
    
    a power ASTNode.
  - pow
```
public static ASTNode pow(ASTNode basis,
                          double exponent)
```
    Creates a power ASTNode.
    
    Parameters:
    
    basis - the basis
    
    exponent - the exponent
    
    Returns:
    
    a power ASTNode.
  - pow
```
public static ASTNode pow(ASTNode basis,
                          int exponent)
```
    Creates a power ASTNode.
    
    Parameters:
    
    basis - the basis
    
    exponent - the exponent
    
    Returns:
    
    a power ASTNode.
  - pow
```
public static ASTNode pow(MathContainer container,
                          CallableSBase basis,
                          CallableSBase exponent)
```
    Raises the given basis by the power of the given exponent.
    
    Parameters:
    
    container - the parent object
    
    basis - the basis
    
    exponent - the exponent
    
    Returns:
    
    a power ASTNode.
  - readMathMLFromString
```
public static ASTNode readMathMLFromString(java.lang.String xml)
```
    Reads the MathML from the given XML string.
    Constructs a corresponding abstract syntax tree, and returns a pointer to the root of the tree.
    
    Parameters:
    
    xml - the MathML XML string.
    
    Returns:
    
    an ASTNode
  - relational
```
private static ASTNode relational(ASTNode.Type type,
                                  ASTNode left,
                                  ASTNode right)
```
    Creates a relational ASTNode of the given type with the two given children left and right.
    Sets the parent SBML object of all nodes to the one provided by the left child.
    
    Parameters:
    
    type - the type of relational node.
    
    left - the left child.
    
    right - the right child.
    
    Returns:
    
    a relational ASTNode of the given type with the two given children left and right.
  - root
```
public static ASTNode root(ASTNode rootExponent,
                           ASTNode radicand)
```
    Creates a root ASTNode.
    
    Parameters:
    
    radicand - the radicand
    
    rootExponent - the exponent of the root element.
    
    Returns:
    
    a root ASTNode.
  - setParentSBMLObject
```
static void setParentSBMLObject(ASTNode node,
                                MathContainer parent)
```
    Sets the Parent of the node and its children to the given value
    
    Parameters:
    
    node - the orphan node
    
    parent - the parent
  - setParentSBMLObject
```
private static void setParentSBMLObject(ASTNode node,
                                        MathContainer parent,
                                        int depth)
```
    Sets the parent of the node and its children to the given value
    
    Parameters:
    
    node - the orphan node
    
    parent - the parent
    
    depth - the current depth in the ASTNode tree. It is just here for testing purposes to track the depth in the tree during the process.
  - sqrt
```
public static ASTNode sqrt(ASTNode radicand)
```
    Creates a root ASTNode.
    
    Parameters:
    
    radicand -
    
    Returns:
    
    a root ASTNode.
  - sum
```
public static ASTNode sum(ASTNode... ast)
```
    Creates a new ASTNode of type Plus with the given nodes as children.
    
    Parameters:
    
    ast - the children nodes.
    
    Returns:
    
    a new ASTNode of type Plus with the given nodes as children.
  - sum
```
public static ASTNode sum(MathContainer parent,
                          CallableSBase... sbase)
```
    Sum of several NamedSBase objects.
    
    Parameters:
    
    parent - the parent
    
    sbase -
    
    Returns:
    
    the sum of several NamedSBase objects.
  - times
```
public static ASTNode times(ASTNode... ast)
```
    Creates an ASTNode of type times and adds the given nodes as children.
    
    Parameters:
    
    ast -
    
    Returns:
    
    an ASTNode of type times and adds the given nodes as children.
  - times
```
public static ASTNode times(MathContainer parent,
                            CallableSBase... sbase)
```
    Multiplies several CallableSBase objects.
    
    Parameters:
    
    parent -
    
    sbase -
    
    Returns:
    
    the multiplication of several CallableSBase objects.
  - uMinus
```
public static ASTNode uMinus(ASTNode ast)
```
    Creates a new ASTNode that has exactly one child and which is of type minus, i.e., this negates what is encoded in ast.
    
    Parameters:
    
    ast -
    
    Returns:
    
    a new ASTNode that has exactly one child and which is of type minus, i.e., this negates what is encoded in ast.
  - uMinus
```
public static ASTNode uMinus(MathContainer container,
                             CallableSBase sbase)
```
    Creates a new ASTNode that has exactly one child and which is of type minus, i.e., this negates what is encoded in ast.
    
    Parameters:
    
    container -
    
    sbase -
    
    Returns:
    
    a new ASTNode that has exactly one child and which is of type minus, i.e., this negates what is encoded in ast.
  - addChild
```
public void addChild(ASTNode child)
```
    Adds a child to this node.
    
    Parameters:
    
    child - the node to add as child.
  - arithmeticOperation
```
private void arithmeticOperation(ASTNode.Type operator,
                                 ASTNode astnode)
```
    Creates a new node with the type of this node, moves all children of this node to this new node, sets the type of this node to the given operator, adds the new node as left child of this node and the given ASTNode as the right child of this node. The parentSBMLObject of the whole resulting ASTNode is then set to the parent of this node.
    Parameters:
    
    operator - The new type of this node. This has to be one of the following: ASTNode.Type.PLUS, ASTNode.Type.MINUS, ASTNode.Type.TIMES, ASTNode.Type.DIVIDE, ASTNode.Type.POWER, ASTNode.Type.FUNCTION_ROOT. Otherwise an IllegalArgumentException is thrown.
    
    astnode - The new right child of this node
    
    Throws:
    java.lang.IllegalArgumentException - if
    
    this ASTNode is zero (isZero()) and the given operator is ASTNode.Type.DIVIDE
    
    the operator is not one of the following: ASTNode.Type.PLUS, ASTNode.Type.MINUS, ASTNode.Type.TIMES, ASTNode.Type.DIVIDE, ASTNode.Type.POWER, ASTNode.Type.FUNCTION_ROOT
  - clone
```
public ASTNode clone()
```
    Specified by:
    
    clone in class AbstractTreeNode
  - compile
```
public ASTNodeValue compile(ASTNodeCompiler compiler)
                     throws SBMLException
```
    Compiles this ASTNode and returns the result.
    
    Parameters:
    
    compiler - An instance of an ASTNodeCompiler that provides methods to translate this ASTNode into something different.
    
    Returns:
    
    Some value wrapped in an ASTNodeValue. The content of the wrapper depends on the ASTNodeCompiler used to create it. However, this ASTNode will ensure that level and version are set appropriately according to this node's parent SBML object.
    
    Throws:
    
    SBMLException - Thrown if an error occurs during the compilation process.
  - containsUndeclaredUnits
```
public boolean containsUndeclaredUnits()
```
    Returns true or false depending on whether this ASTNode refers to elements such as parameters or numbers with undeclared units. A return value of true indicates that the UnitDefinition returned by SBaseWithDerivedUnit.getDerivedUnitDefinition() may not accurately represent the units of the expression.
    
    Returns:
    
    true if the math expression of this ASTNode includes parameters/numbers with undeclared units, false otherwise.
  - deriveUnit
```
public UnitDefinition deriveUnit()
                          throws SBMLException
```
    Evaluates recursively this ASTNode and creates a new UnitDefinition with respect of all referenced elements.
    
    Returns:
    
    the derived unit of the node.
    
    Throws:
    
    SBMLException - if they are problems going through the ASTNode tree.
  - divideBy
```
public ASTNode divideBy(ASTNode ast)
```
    Divides this node by the given node
    
    Parameters:
    
    ast - an ASTNode
    
    Returns:
    
    the current node for convenience.
  - divideBy
```
public ASTNode divideBy(CallableSBase namedSBase)
```
    Divides this node by the given SBML element.
    
    Parameters:
    
    namedSBase - an SBML element that can be represented by a value.
    
    Returns:
    
    the current node for convenience.
  - equals
```
public boolean equals(java.lang.Object object)
```
    Overrides:
    
    equals in class AbstractTreeNode
  - findReferencedGlobalParameters
```
public java.util.List<Parameter> findReferencedGlobalParameters()
```
    Goes through the formula and identifies all global parameters that are referenced by this rate equation.
    
    Returns:
    
    all global parameters that are referenced by this rate equation.
  - getAllowsChildren
```
public boolean getAllowsChildren()
```
  - getCharacter
```
public char getCharacter()
```
    Gets the value of this node as a single character. This function should be called only when ASTNode.getType() is one of PLUS, MINUS, TIMES, DIVIDE or POWER.
    
    Returns:
    
    the value of this ASTNode as a single character
    
    Throws:
    
    java.lang.IllegalArgumentException - if the type of the node is not one of PLUS, MINUS, TIMES, DIVIDE or POWER.
  - getChild
```
public ASTNode getChild(int index)
```
    Gets a child of this node according to an index number.
    
    Parameters:
    
    index - the index of the child to get
    
    Returns:
    
    the child of this ASTNode with the given index.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - - if the index is out of range (index < 0 || index >= size()).
  - getChildAt
```
public javax.swing.tree.TreeNode getChildAt(int i)
```
  - getChildCount
```
public int getChildCount()
```
  - getChildren
```
public java.util.List<ASTNode> getChildren()
```
    Returns the list of children of the current ASTNode.
    
    Returns:
    
    the list of children of the current ASTNode.
  - getClassName
```
public java.lang.String getClassName()
```
    Returns the class name of the mathML element represented by this ASTNode.
    
    Returns:
    
    the class name of the mathML element represented by this ASTNode.
  - getDefinitionURL
```
public java.lang.String getDefinitionURL()
```
    Returns the definitionURL
    
    Returns:
    
    the definitionURL
  - getDenominator
```
public int getDenominator()
```
    Gets the value of the denominator of this node. This function should be called only when getType() == RATIONAL, otherwise an Exception is thrown.
    
    Returns:
    
    the value of the denominator of this ASTNode.
    
    Throws:
    
    java.lang.IllegalArgumentException - if the method is called on a node that is not of type rational.
  - getEncoding
```
public java.lang.String getEncoding()
```
    Returns the encoding of the mathML element represented by this ASTNode.
    
    Returns:
    
    the encoding of the mathML element represented by this ASTNode.
  - getExponent
```
public int getExponent()
```
    Gets the exponent value of this ASTNode. This function should be called only when getType() returns REAL_E or REAL, otherwise an Exception is thrown.
    
    Returns:
    
    the value of the exponent of this ASTNode.
    
    Throws:
    
    java.lang.IllegalArgumentException - if the method is called on a node that is not of type real.
  - getId
```
public java.lang.String getId()
```
    Returns the id of the mathML element represented by this ASTNode.
    
    Returns:
    
    the id of the mathML element represented by this ASTNode.
  - getInteger
```
public int getInteger()
```
    Gets the value of this node as an integer. This function should be called only when getType() == INTEGER, otherwise an Exception is thrown.
    
    Returns:
    
    the value of this ASTNode as an integer.
    
    Throws:
    
    java.lang.IllegalArgumentException - if the node is not of type integer.
  - getLeftChild
```
public ASTNode getLeftChild()
```
    Gets the left child of this node.
    
    Returns:
    
    the left child of this ASTNode. This is equivalent to getChild(0);
  - getListOfNodes
```
public java.util.List<ASTNode> getListOfNodes()
```
    Returns the list of children of the current ASTNode.
    
    Returns:
    
    the list of children of the current ASTNode.
  - getListOfNodes
```
public java.util.List<ASTNode> getListOfNodes(Filter filter)
```
    Returns the list of children of the current ASTNode that satisfy the given filter.
    
    Parameters:
    
    filter -
    
    Returns:
    
    the list of children of the current ASTNode that satisfy the given filter.
  - getMantissa
```
public double getMantissa()
```
    Gets the mantissa value of this node. This function should be called only when getType() returns REAL_E or REAL, otherwise an Exception is thrown. If getType() returns REAL, this method is identical to getReal().
    
    Returns:
    
    the value of the mantissa of this ASTNode.
  - getName
```
public java.lang.String getName()
```
    Gets the name of this node. This method may be called on nodes that are not operators (isOperator() == false) or numbers (isNumber() == false).
    
    Returns:
    
    the name of this node.
    
    Throws:
    
    java.lang.IllegalArgumentException - if the method is called on nodes that are operators or numbers.
  - getNumerator
```
public int getNumerator()
```
    Gets the value of the numerator of this node. This method should be called only when getType() == RATIONAL, otherwise an Exception is thrown.
    
    Returns:
    
    the value of the numerator of this ASTNode.
    
    Throws:
    
    java.lang.IllegalArgumentException - if this method is called on a node type other than rational.
  - getParent
```
public javax.swing.tree.TreeNode getParent()
```
    Specified by:
    
    getParent in interface javax.swing.tree.TreeNode
    
    Overrides:
    
    getParent in class AbstractTreeNode
  - getParentSBMLObject
```
public MathContainer getParentSBMLObject()
```
    This method is convenient when holding an object nested inside other objects in an SBML model. It allows direct access to the MathContainer; element containing it. From this MathContainer even the overall Model can be accessed.
    
    Returns:
    
    the parent SBML object.
  - getReal
```
public double getReal()
```
    Gets the real-numbered value of this node. This function should be called only when isReal() == true, otherwise and Exception is thrown. This function performs the necessary arithmetic if the node type is REAL_E (mantissa^exponent) or RATIONAL (numerator / denominator).
    
    Returns:
    
    the value of this ASTNode as a real (double).
    
    Throws:
    
    java.lang.IllegalArgumentException - if this node is not of type real.
  - getReferencedNamedSBases
```
public java.util.Set<NamedSBase> getReferencedNamedSBases()
```
    Returns a set of all the NamedSBase referenced on this node and all his descendant. Just for testing purposes...
    
    Returns:
    
    a set of all the NamedSBase referenced on this node and all his descendant.
  - getRightChild
```
public ASTNode getRightChild()
```
    Returns the last child in the list of children of this node.
    
    Returns:
    
    This is equivalent to calling getListOfNodes().getLast().
  - getStyle
```
public java.lang.String getStyle()
```
    Returns the style of the mathML element represented by this ASTNode.
    
    Returns:
    
    the style of the mathML element represented by this ASTNode.
  - getType
```
public ASTNode.Type getType()
```
    Returns the type of this node.
    
    Returns:
    
    the type of this node.
  - getUnits
```
public java.lang.String getUnits()
```
    Returns the units attribute.
    
    Returns:
    
    the units attribute.
  - getUnitsInstance
```
public UnitDefinition getUnitsInstance()
```
    Creates or obtains a UnitDefinition corresponding to the unit that has been set for this ASTNode and returns a pointer to it. Note that in case that this ASTNode is associated with a Unit.Kind, the created UnitDefinition will not be part of the model, it is just a container for the Unit.Kind.
    
    Returns:
    
    A UnitDefinition or null.
  - getVariable
```
public CallableSBase getVariable()
```
    Returns the variable of this node. This function should be called only when isVariable() == true}, otherwise an Exception is thrown.
    
    Returns:
    
    the variable of this node
    
    Throws:
    
    java.lang.RuntimeException - if isVariable() returns false.
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class AbstractTreeNode
  - hasUnits
```
public boolean hasUnits()
```
    Returns true if the current ASTNode or any of his descendant has a unit defined.
    
    Returns:
    
    true if the current ASTNode or any of his descendant has a unit defined.
  - initDefaults
```
private void initDefaults()
```
    Initializes the default values/attributes of the node.
  - insertChild
```
public void insertChild(int n,
                        ASTNode newChild)
```
    Inserts the given ASTNode at point n in the list of children of this ASTNode. Inserting a child within an ASTNode may result in an inaccurate representation.
    
    Parameters:
    
    n - long the index of the ASTNode being added
    
    newChild - ASTNode to insert as the n^th child
  - isBoolean
```
public boolean isBoolean()
```
    Returns true 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.
  - isConstant
```
public boolean isConstant()
```
    Returns true if this node represents a MathML constant (e.g., true, Pi).
    
    Returns:
    
    true if this ASTNode is a MathML constant, false otherwise.
  - isDifference
```
public boolean isDifference()
```
    Checks if this ASTNode represents a difference.
    
    Returns:
    
    true if this ASTNode represents a difference, false otherwise.
  - isFunction
```
public boolean isFunction()
```
    Returns true if this node represents a function. In this context, the term function means pre-defined functions such as "ceil", "abs" or "sin" or whether this ASTNode refers to a user-defined FunctionDefinition object. Without having a valid reference to the MathContainer that owns this ASTNode it is impossible to identify the referenced FunctionDefinition.
    
    Returns:
    
    true if this ASTNode is a function, false otherwise.
  - isInfinity
```
public boolean isInfinity()
```
    Returns true if this node represents the special IEEE 754 value infinity, false otherwise.
    
    Returns:
    
    true if this ASTNode is the special IEEE 754 value infinity, false otherwise.
  - isInteger
```
public boolean isInteger()
```
    Returns true if this node contains an integer value, false otherwise.
    
    Returns:
    
    true if this ASTNode is of type INTEGER, false otherwise.
  - isLambda
```
public boolean isLambda()
```
    Returns true if this node is a MathML <lambda>, false otherwise.
    
    Returns:
    
    true if this ASTNode is of type LAMBDA, false otherwise.
  - isLiteral
```
public boolean isLiteral()
```
    Returns true if this node is constant or of type INTEGER, REAL or RATIONAL, false otherwise.
    
    Returns:
    
    true if this ASTNode is constant or of type INTEGER, REAL or RATIONAL, false otherwise.
  - isLog10
```
public boolean isLog10()
```
    Returns true if this node represents a log10() function, false otherwise. More precisely, this predicate returns true if the node type is FUNCTION_LOG with two children, the first of which is an INTEGER equal to 10.
    
    Returns:
    
    true if the given ASTNode represents a log10() function, false otherwise.
  - isLogical
```
public boolean isLogical()
```
    Returns true if this node is a MathML logical operator (i.e., and, or, not, xor).
    
    Returns:
    
    true if this ASTNode is a MathML logical operator.
  - isMinusOne
```
public boolean isMinusOne()
```
    Returns true if this astnode represents the number minus one (either as integer or as real value).
    
    Returns:
    
    true if this astnode represents the number minus one (either as integer or as real value).
  - isName
```
public boolean isName()
```
    Returns true if this node is a user-defined Variable name in SBML L1, L2 (MathML), or the special symbols time, Avogadro or rateOf. The predicate returns false otherwise.
    
    Returns:
    
    true if this ASTNode is a user-defined variable name in SBML L1, L2 (MathML) or the special symbols time, Avogadro or rateOf.
  - isNaN
```
public boolean isNaN()
```
    Returns true if this node is a type Real and represents the special IEEE 754 value 'not a number' Double.NaN, false otherwise.
    
    Returns:
    
    true if this ASTNode is the Double.NaN
  - isNegInfinity
```
public boolean isNegInfinity()
```
    Returns true if this node represents the special IEEE 754 value 'negative infinity' Double.NEGATIVE_INFINITY, false otherwise.
    
    Returns:
    
    true if this ASTNode is Double.NEGATIVE_INFINITY, false otherwise.
  - isNumber
```
public boolean isNumber()
```
    Returns true if this node contains a number, false otherwise. This is functionally equivalent to the following code:
```
 isInteger() || isReal()
 
```
    Returns:
    
    true if this ASTNode is a number, false otherwise.
  - isOne
```
public boolean isOne()
```
    Returns true if this ASTNode represents the number one (either as integer or as real value).
    
    Returns:
    
    true if this ASTNode represents the number one.
  - isOperator
```
public boolean isOperator()
```
    Returns true if this node is a mathematical operator, meaning, +, -, *, / or ^ (power).
    
    Returns:
    
    true if this ASTNode is an operator.
  - isPiecewise
```
public boolean isPiecewise()
```
    Returns true if this node is the MathML <piecewise> construct, false otherwise.
    
    Returns:
    
    true if this ASTNode is a MathML piecewise function
  - isRational
```
public boolean isRational()
```
    Returns true if this node represents a rational number, false otherwise.
    
    Returns:
    
    true if this ASTNode is of type ASTNode.Type.RATIONAL.
  - isReal
```
public boolean isReal()
```
    Returns true if this node can represent a real number, false otherwise. More precisely, this node must be of one of the following types: REAL, REAL_E or RATIONAL.
    
    Returns:
    
    true if the value of this ASTNode can represented a real number, false otherwise.
  - isRelational
```
public boolean isRelational()
```
    Returns true if this node is a MathML relational operator, meaning ==, >=, >, <, <=, and !=.
    
    Returns:
    
    true if this ASTNode is a MathML relational operator, false otherwise.
  - isSemantics
```
public boolean isSemantics()
```
    Return true if this node contain some semantics annotations.
    
    Returns:
    
    true if this node contain some semantics annotations.
    
    See Also:
    
    getNumSemanticsAnnotations()
  - isSetClassName
```
public boolean isSetClassName()
```
    Returns:
  - isSetDefinitionURL
```
public boolean isSetDefinitionURL()
```
    Returns:
  - isSetEncoding
```
public boolean isSetEncoding()
```
    Returns:
  - isSetId
```
public boolean isSetId()
```
    Returns:
  - isSetName
```
public boolean isSetName()
```
    Returns:
  - isSetNumberType
```
public boolean isSetNumberType()
```
    Returns true if the number type is set.
    
    Returns:
    
    true if the number type is set.
  - isSetParentSBMLObject
```
public boolean isSetParentSBMLObject()
```
    Checks if a parent SBML object, i.e., a MathContainer, is set as a parent SBML object for this ASTNode.
    
    Returns:
  - isSetStyle
```
public boolean isSetStyle()
```
    Returns:
  - isSetUnits
```
public boolean isSetUnits()
```
    Returns true if a unit is defined on this node.
    
    Returns:
    
    true if a unit is defined on this node.
  - isSqrt
```
public boolean isSqrt()
```
    Returns true if this node represents a square root function, false otherwise. More precisely, the node type must be ASTNode.Type.FUNCTION_ROOT with two children, the first of which is an ASTNode.Type.INTEGER node having value equal to 2.
    
    Returns:
    
    true if the given ASTNode represents a sqrt() function, false otherwise.
  - isString
```
public boolean isString()
```
    Returns true if this node is a name or refers to a FunctionDefinition.
    
    Returns:
    
    true if this ASTNode is a user-defined variable name in SBML L1, L2 (MathML) or the special symbols time or Avogadro.
    
    See Also:
    
    isName()
  - isSum
```
public boolean isSum()
```
    Checks if this ASTNode represents a sum.
    
    Returns:
    
    true if this ASTNode represents a sum, false otherwise.
  - isUMinus
```
public boolean isUMinus()
```
    Returns true if this node is a unary minus operator, false otherwise. A node is defined as a unary minus node if it is of type 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 parse. However, unary minus nodes for symbols (NAMES) cannot be 'collapsed', so this predicate function is necessary.
    
    Returns:
    
    true if this ASTNode is a unary minus, false otherwise.
  - isUnary
```
public boolean isUnary()
```
    Checks whether the number of child nodes is exactly one.
    
    Returns:
    
    true if the number of child nodes is exactly one.
  - isUnknown
```
public boolean isUnknown()
```
    Returns true if this node has an ASTNode.Type.UNKNOWN type. 'Unknown' nodes have the type ASTNode.Type.UNKNOWN. Nodes with unknown types will not appear in an ASTNode tree returned by JSBML based upon valid SBML input; the only situation in which a node with type UNKNOWN may appear is immediately after having created 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 ASTNode.Type.UNKNOWN, false otherwise.
  - isVariable
```
public boolean isVariable()
```
    Returns true if this node represents a Variable.
    
    Returns:
    
    true if this node represents a Variable.
  - isVector
```
public boolean isVector()
```
    Checks if this ASTNode represents a vector.
    
    Returns:
    
    true if this ASTNode represents a vector, false otherwise.
  - isZero
```
public boolean isZero()
```
    Returns true if this node represents the number zero (either as integer or as real value).
    
    Returns:
    
    true if this node represents the number zero.
  - minus
```
public ASTNode minus(ASTNode ast)
```
    Subtracts the given ASTNode from this node.
    
    Parameters:
    
    ast - an ASTNode
    
    Returns:
    
    the current node for convenience.
  - minus
```
public ASTNode minus(double real)
```
    Subtracts the given number from this node.
    
    Parameters:
    
    real - a double number.
    
    Returns:
    
    the current node for convenience.
  - minus
```
public ASTNode minus(int integer)
```
    Subtracts the given integer from this node.
    
    Parameters:
    
    integer - an integer number.
    
    Returns:
    
    the current node for convenience.
  - minus
```
public ASTNode minus(int integer,
                     java.lang.String unitsID)
```
    Parameters:
    
    integer -
    
    unitsID -
    
    Returns:
  - multiplyWith
```
public ASTNode multiplyWith(ASTNode ast)
```
    Multiplies this ASTNode with the given node
    
    Parameters:
    
    ast - an ASTNode
    
    Returns:
    
    the current node for convenience.
  - multiplyWith
```
public ASTNode multiplyWith(ASTNode... nodes)
```
    Multiplies this ASTNode with the given nodes, i.e., all given nodes will be children of this node, whose type will be set to ASTNode.Type.TIMES.
    
    Parameters:
    
    nodes - some ASTNode
    
    Returns:
    
    The current node for convenience.
  - multiplyWith
```
public ASTNode multiplyWith(CallableSBase nsb)
```
    Multiplies this ASTNode with the given SBML element.
    
    Parameters:
    
    nsb - an SBML element that can be represented by a value.
    
    Returns:
    
    the current node for convenience.
  - plus
```
public ASTNode plus(ASTNode ast)
```
    Adds a given node to this node.
    
    Parameters:
    
    ast - an ASTNode
    
    Returns:
    
    the current node for convenience.
  - plus
```
public ASTNode plus(CallableSBase nsb)
```
    Adds an SBML element to this node.
    
    Parameters:
    
    nsb - an SBML element that can be represented by a value.
    
    Returns:
    
    the current node for convenience.
  - plus
```
public ASTNode plus(double real)
```
    Adds a number to this node.
    
    Parameters:
    
    real - a double number.
    
    Returns:
    
    the current node for convenience.
  - plus
```
public ASTNode plus(int integer)
```
    Adds an integer number to this node.
    
    Parameters:
    
    integer - an integer number.
    
    Returns:
    
    the current node for convenience.
  - prependChild
```
public void prependChild(ASTNode child)
```
    Adds the given node as a child of this ASTNode. This method adds child nodes from right to left.
    
    Parameters:
    
    child - an ASTNode
  - raiseByThePowerOf
```
public ASTNode raiseByThePowerOf(ASTNode exponent)
```
    Raises this ASTNode by the power of the value of the given node.
    
    Parameters:
    
    exponent - an ASTNode
    
    Returns:
    
    the current node for convenience.
  - raiseByThePowerOf
```
public ASTNode raiseByThePowerOf(CallableSBase nsb)
```
    Raises this ASTNode by the power of the value of this named SBase object.
    
    Parameters:
    
    nsb - an SBML element that can be represented by a value.
    
    Returns:
    
    the current node for convenience.
  - raiseByThePowerOf
```
public ASTNode raiseByThePowerOf(double exponent)
```
    Raises this ASTNode by the power of the given number.
    
    Parameters:
    
    exponent - a double number.
    
    Returns:
    
    the current node for convenience.
  - reduceToBinary
```
private void reduceToBinary()
```
    Reduces this ASTNode to a binary tree, e.g., if the formula in this ASTNode is and(x, y, z) then the formula of the reduced node would be and(and(x, y), z).
    
    This method is not yet completed. Currently, only ASTNode.Type.PLUS, ASTNode.Type.TIMES, ASTNode.Type.LOGICAL_AND, ASTNode.Type.LOGICAL_OR are touched by the method. All other nodes are left unchanged, but it traverses the entire tree rooted at this node.
  - refersTo
```
public boolean refersTo(java.lang.String id)
```
    Returns true if this node or one of its descendants contains some identifier with the given id. This method can be used to scan a formula for a specific parameter or species and detect whether this component is used by this formula. This search is done using a DFS.
    
    Parameters:
    
    id - the id of an SBML element.
    
    Returns:
    
    true if this node or one of its descendants contains the given id.
  - removeChild
```
public boolean removeChild(int n)
```
    Removes child n of this ASTNode. Removing a child from an ASTNode may result in an inaccurate representation.
    
    Parameters:
    
    n - the index of the child to remove
    
    Returns:
    
    boolean indicating the success or failure of the operation
  - replaceArgument
```
public void replaceArgument(java.lang.String bvar,
                            ASTNode arg)
```
    Replaces occurrences of a name within this ASTNode with the name/value/formula represented by the second argument ASTNode, e.g., if the formula in this ASTNode is x + y; bvar is x and arg is an ASTNode representing the real value 3 ReplaceArgument substitutes 3 for x within this ASTNode.
    
    Parameters:
    
    bvar - a string representing the variable name to be substituted
    
    arg - an ASTNode representing the name/value/formula to substitute
  - replaceChild
```
public ASTNode replaceChild(int n,
                            ASTNode newChild)
```
    Replaces the n^th child of this ASTNode with the given ASTNode.
    
    Parameters:
    
    n - long the index of the child to replace
    
    newChild - ASTNode to replace the n^th child
    
    Returns:
    
    the element previously at the specified position
  - resetParentSBMLObject
```
private void resetParentSBMLObject(ASTNode node)
```
    Resets the parentSBMLObject to null recursively.
    
    Parameters:
    
    node -
  - setCharacter
```
public void 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 UNKNOWN.
    
    Parameters:
    
    value - the character value to which the node's value should be set.
  - setClassName
```
public void setClassName(java.lang.String className)
```
    Sets the class name of the mathML element represented by this ASTNode.
    
    Parameters:
    
    className - the class name.
  - setDefinitionURL
```
public void setDefinitionURL(java.lang.String definitionURL)
```
    Parameters:
    
    definitionURL -
  - setEncoding
```
public void setEncoding(java.lang.String encoding)
```
    Sets the encoding of the mathML element represented by this ASTNode.
    
    Parameters:
    
    encoding - the encoding
  - setId
```
public void setId(java.lang.String id)
```
    Sets the id of the mathML element represented by this ASTNode.
    
    Parameters:
    
    id - the id.
  - setIsSetNumberType
```
public void setIsSetNumberType(boolean isSetNumberType)
```
    Parameters:
    
    isSetNumberType -
  - setName
```
public void setName(java.lang.String name)
```
    Sets the value of this ASTNode to the given name. The node type will be set (to ASTNode.Type.NAME) only if the ASTNode was previously an operator (isOperator(node) == true) or number (isNumber(node) == true). This allows names to be set for ASTNode.Type.FUNCTIONs and the like.
    
    Parameters:
    
    name -
  - setParentSBMLObject
```
public void setParentSBMLObject(MathContainer parent)
```
    Sets the Parent of the node to the given value
    
    Parameters:
    
    parent - the parent
  - setStyle
```
public void setStyle(java.lang.String style)
```
    Sets the style of the mathML element represented by this ASTNode.
    
    Parameters:
    
    style - the style.
  - setType
```
public void setType(java.lang.String typeStr)
```
    Sets the type from a String. The method accept all the supported mathML elements, the possible types of cn elements or the possible definitionURL of csymbol elements.
    
    Parameters:
    
    typeStr - the type as a String.
  - setType
```
public void setType(ASTNode.Type type)
```
    Sets the type of this ASTNode to the given Type. A side-effect of doing this is that any numerical values previously stored in this node are reset to zero.
    
    Parameters:
    
    type - the type to which this node should be set
  - setUnits
```
public void setUnits(java.lang.String unitId)
```
    Sets the units attribute.
    
    Parameters:
    
    unitId -
    
    Throws:
    
    java.lang.IllegalArgumentException - if the ASTNode is not a kind of numbers (<cn> in mathml) or if the unitId is not a valid unit kind or the id of a unit definition.
  - setUnits
```
public void setUnits(Unit.Kind unit)
```
    Parameters:
    
    unit -
  - setUnits
```
public void setUnits(UnitDefinition ud)
```
    Parameters:
    
    ud -
  - setValue
```
public void setValue(double value)
```
    Sets the value of this ASTNode to the given double number and sets the node type to REAL. This is functionally equivalent to:
```
 setValue(value, 0);
 
```
    Parameters:
    
    value - the double format number to which this node's value should be set
  - setValue
```
public void setValue(double mantissa,
                     int 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 REAL_E.
    
    Parameters:
    
    mantissa - the mantissa of this node's real-numbered value
    
    exponent - the exponent of this node's real-numbered value
  - setValue
```
public void setValue(int value)
```
    Sets the value of this ASTNode to the given (long) integer and sets the node type to INTEGER.
    
    Parameters:
    
    value -
  - setValue
```
public void setValue(int numerator,
                     int denominator)
```
    Sets the value of this ASTNode to the given rational in two parts: the numerator and denominator. The node type is set to RATIONAL.
    
    Parameters:
    
    numerator - the numerator value of the rational
    
    denominator - the denominator value of the rational
  - setVariable
```
public void setVariable(CallableSBase variable)
```
    Allows you to directly set an instance of CallableSBase as the variable of this ASTNode. Note that if the given variable does not have a declared id field, the pointer to this variable will get lost when cloning this node. Only references to identifiers are permanently stored. The pointer can also not be written to an SBML file without a valid identifier.
    
    Parameters:
    
    variable - a pointer to a CallableSBase.
  - sqrt
```
public ASTNode sqrt()
```
    Applies the square root function on this syntax tree and returns the resulting tree.
    
    Returns:
    
    the current node for convenience.
  - swapChildren
```
public void swapChildren(ASTNode that)
```
    Swaps the children of this ASTNode with the children of that ASTNode.
    
    Unfortunately, when swapping child nodes, we have to recursively traverse the entire subtrees in order to make sure that all pointers to the parent SBML object are correct. However, this must only be done if the parent SBML object of that differs from the one surrounding this node.
    
    In any case, the pointer from each sub-node to its parent must be changed. In contrast to other SBML elements, ASTNodes have sub-nodes as direct children, i.e., there is no child called 'ListOfNodes'. The setParent method is also not recursive.
    
    However, this might cause many calls to listeners.
    
    Parameters:
    
    that - the other node whose children should be used to replace this node's children
  - toASTNode2
```
public ASTNode2 toASTNode2()
```
    Return the ASTNode2 corresponding to the current ASTNode
    
    Returns:
    
    node ASTNode2
  - toFormula
```
public java.lang.String toFormula()
                           throws SBMLException
```
    Converts this ASTNode to a text string using a specific syntax for mathematical formulas.
    The text-string form of mathematical formulas produced by toFormula() and read by parseFormula() are simple C-inspired infix notation taken from SBML Level 1. A formula in this text-string form therefore can be handed to a program that understands SBML Level 1 mathematical expressions, or used as part of a formula translation system. Be careful that the default FormulaCompilerLibSBML used produce an output a bit different than pure SBML level 1 mathematical expressions, in particular for logical and relational operators.
    
    Returns:
    
    the formula representing this ASTNode as an SBML Level 1 text-string mathematical formula.
    
    Throws:
    
    SBMLException - if there is a problem in the ASTNode tree.
  - toFormula
```
public java.lang.String toFormula(FormulaCompiler compiler)
                           throws SBMLException
```
    Converts this ASTNode to a text string using a specific FormulaCompiler.
    
    Parameters:
    
    compiler -
    
    Returns:
    
    the formula representing this ASTNode. null is returned if the given compiler is null.
    
    Throws:
    
    SBMLException - if there is a problem in the ASTNode tree.
    
    See Also:
    
    FormulaCompiler, FormulaCompilerLibSBML
  - toLaTeX
```
public java.lang.String toLaTeX()
                         throws SBMLException
```
    Converts this node recursively into a LaTeX formatted String.
    
    Returns:
    
    A String representing the LaTeX code necessary to write the formula corresponding to this node in a document.
    
    Throws:
    
    SBMLException - if there is a problem in the ASTNode tree.
  - toMathML
```
public java.lang.String toMathML()
```
    Converts this node recursively into a MathML string that corresponds to the subset of MathML defined in the SBML specification.
    
    Returns:
    
    the representation of this node in MathML.
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class AbstractTreeNode
  - printASTNode
```
public java.lang.String printASTNode()
```
    Returns the infix formula representing this ASTNode or an empty String if there was a problem to construct the formula.
    
    Returns:
    
    the infix formula representing this ASTNode
  - toSimpleString
```
public java.lang.String toSimpleString()
```
    Returns a simple String representing the content of the ASTNode.
    
    Returns:
    
    a simple String representing the content of the ASTNode.
  - unsetUnits
```
public void unsetUnits()
```
    Unset the units attribute.
  - updateVariables
```
public void updateVariables()
```
    For a better performance ASTNodes can store a direct pointer to a variable element. This is particularly useful when performing more complex computation on these data structures. However, if the model is changed, it may happen that these pointer become invalid. For instance, a previously local parameter may be added to the model in form of a global parameter while keeping the same identifier. The local parameter may then be removed. Whenever performing changes like this, you may want to update pointers within ASTNode constructs as well.
  - astNodeToTree
```
public static java.lang.String astNodeToTree(ASTNode n,
                                             java.lang.String tree,
                                             java.lang.String indent)
```
    Returns a simple tree view of the ASTNode internal, including mainly node type and hierarchy.
    
    Parameters:
    
    n -
    
    tree -
    
    indent -
    
    Returns:
    
    a simple tree view of the ASTNode internal
  - addSemanticsAnnotation
```
public XMLNode addSemanticsAnnotation(XMLNode semanticsAnnotation)
```
    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:
    
    semanticsAnnotation - the annotation to add.
    
    Returns:
    
    the added XMLNode.
  - getNumSemanticsAnnotations
```
public int getNumSemanticsAnnotations()
```
    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:
    
    addSemanticsAnnotation(XMLNode semanticsAnnotation)
  - getSemanticsAnnotation
```
public XMLNode getSemanticsAnnotation(int n)
```
    Gets the nth <semantics> 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 or n < 0).
    
    See Also:
    
    addSemanticsAnnotation(XMLNode sAnnotation)
  - getListOfSemanticsAnnotations
```
public java.util.List<XMLNode> getListOfSemanticsAnnotations()
```
    Returns the list of semantics annotations of this node.
    
    Returns:
    
    the list of semantics annotations of this node or null if no semantics annotation are present.
  - createPlugin
```
public ASTNodePlugin createPlugin(java.lang.String nameOrUri)
```
    Creates a new ASTNodePlugin for the given package name or URI and adds it to this ASTNode.
    If an ASTNodePlugin was already present in this ASTNode it will be replaced.
    
    Parameters:
    
    nameOrUri - the package name or URI
    
    Returns:
    
    a new ASTNodePlugin for the given package name or URI
  - addExtension
```
public void addExtension(java.lang.String nameOrUri,
                         ASTNodePlugin sbasePlugin)
```
    Adds a ASTNodePlugin object to this ASTNode.
    If a previous ASTNodePlugin associated with the same package was present before, it will be replaced.
    
    Parameters:
    
    nameOrUri - the name or URI of the package extension.
    
    sbasePlugin - the ASTNodePlugin to add.
  - addPlugin
```
public void addPlugin(java.lang.String nameOrUri,
                      ASTNodePlugin sbasePlugin)
```
    Adds a ASTNodePlugin object to this ASTNode.
    If a previous ASTNodePlugin associated with the same package was present before, it will be replaced.
    
    Parameters:
    
    nameOrUri - the name or URI of the package extension.
    
    sbasePlugin - the ASTNodePlugin to add.
    
    See Also:
    
    addExtension(String, ASTNodePlugin)
  - disablePackage
```
public void disablePackage(java.lang.String packageURIOrName)
```
    Disables the given SBML Level 3 package on this SBMLDocument.
    
    Parameters:
    
    packageURIOrName - a package namespace URI or package name
  - enablePackage
```
public void enablePackage(java.lang.String packageURIOrName)
```
    Enables the given SBML Level 3 package on this SBMLDocument.
    
    Parameters:
    
    packageURIOrName - a package namespace URI or package name
  - enablePackage
```
public void enablePackage(java.lang.String packageURIOrName,
                          boolean enabled)
```
    Enables or disables the given SBML Level 3 package on this SBMLDocument.
    
    Parameters:
    
    packageURIOrName - a package namespace URI or package name
    
    enabled - a boolean to tell if the package need to be enabled or disabled. It true the package will be enabled, otherwise it will be disabled.
  - getExtension
```
public ASTNodePlugin getExtension(java.lang.String nameOrUri)
```
    Returns the ASTNodePlugin object which matches this package name or URI.
    
    Parameters:
    
    nameOrUri - the package name or URI
    
    Returns:
    
    the ASTNodePlugin object which matches this package name or URI, null is returned if nothing matching the name or URI is found.
  - getExtensionCount
```
public int getExtensionCount()
```
    Returns the number of ASTNodePlugins of this ASTNode.
    
    Returns:
    
    the number of ASTNodePlugins of this ASTNode.
  - getNumPlugins
```
public int getNumPlugins()
```
    Returns the number of ASTNodePlugins of this ASTNode.
    
    Returns:
    
    the number of ASTNodePlugins of this ASTNode.
  - getPlugin
```
public ASTNodePlugin getPlugin(java.lang.String nameOrUri)
```
    Returns an ASTNodePlugin for an SBML Level 3 package extension with the given package name or URI.
    If no ASTNodePlugin is found for this package, a new ASTNodePlugin is created, added to this ASTNode and returned.
    
    Parameters:
    
    nameOrUri - the name or URI of the package
    
    Returns:
    
    an ASTNodePlugin for an SBML Level 3 package extension with the given package name or URI.
  - isExtendedByOtherPackages
```
public boolean isExtendedByOtherPackages()
```
    Returns true if this object is extended by other packages.
    
    Returns:
    
    true if this object is extended by other packages.
  - isPackageEnabled
```
public boolean isPackageEnabled(java.lang.String packageURIOrName)
```
    Returns true if the given SBML Level 3 package is enabled within the containing SBMLDocument.
    
    Parameters:
    
    packageURIOrName - the name or URI of the package extension.
    
    Returns:
    
    true if the given SBML Level 3 package is enabled within the containing SBMLDocument, false otherwise.
  - isPackageURIEnabled
```
public boolean isPackageURIEnabled(java.lang.String packageURIOrName)
```
    Returns true if the given SBML Level 3 package is enabled within the containing SBMLDocument.
    
    Parameters:
    
    packageURIOrName - the name or URI of the package extension.
    
    Returns:
    
    true if the given SBML Level 3 package is enabled within the containing SBMLDocument, false otherwise.
    
    See Also:
    
    isPackageEnabled(String)
  - isSetPlugin
```
public boolean isSetPlugin(java.lang.String nameOrUri)
```
    Returns true if an ASTNodePlugin is defined for the given package.
    
    Parameters:
    
    nameOrUri - the package name or URI
    
    Returns:
    
    true if an ASTNodePlugin is defined for the given package.
  - unsetExtension
```
public void unsetExtension(java.lang.String nameOrUri)
```
    Unsets the ASTNodePlugin extension object which matches this package name or URI.
    
    Parameters:
    
    nameOrUri - the package name or URI
  - unsetPlugin
```
public void unsetPlugin(java.lang.String nameOrUri)
```
    Unsets the ASTNodePlugin plugin object which matches this package name or URI.
    
    Parameters:
    
    nameOrUri - the package name or URI
    
    See Also:
    
    unsetExtension(String)
  - getExtensionPackages
```
public java.util.Map<java.lang.String,ASTNodePlugin> getExtensionPackages()
```
    Returns the map containing all the ASTNodePlugin extension objects of this ASTNode.
    
    Returns:
    
    the map containing all the ASTNodePlugin extension objects of this ASTNode.

Class ASTNode

Nested Class Summary

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

Constructor Summary

Method Summary

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

URI_AVOGADRO_DEFINITION

URI_DELAY_DEFINITION

URI_MATHML_DEFINITION

URI_MATHML_PREFIX

URI_RATE_OF_DEFINITION

URI_TIME_DEFINITION

IMPLEMENTATION_HISTORIC

IMPLEMENTATION_ASTNODE2

IMPLEMENTATION_VERSION

definitionURL

denominator

exponent

id

style

className

encoding

semanticsAnnotationList

isSetNumberType

listOfNodes

logger

isDebugEnabled

mantissa

name

numerator

parentSBMLObject

type

unitId

variable

plugins

Constructor Detail

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

ASTNode

Method Detail

abs

abs

arithmethicOperation

diff

eq

exp

formulaToString

formulaToString

frac

frac

frac

frac

geq

gt

leq

log

log

lt

lt

neq