org.sbml.jsbml.math

Class ASTFactory

java.lang.Object

org.sbml.jsbml.math.ASTFactory

public class ASTFactory
extends java.lang.Object

A collection of static methods that can be used to create new abstract syntax trees or alter the topology of existing ones.

Since:

1.0

Version:

$Rev$

Author:

Victor Kofia

Constructor Summary

Constructors

Constructor and Description
ASTFactory()

Method Summary

Modifier and Type	Method and Description
static ASTLogicalOperatorNode	and(ASTNode2... ast) Creates an ASTLogicalOperatorNode of type ASTNode.Type.LOGICAL_AND and adds the given nodes as children.
static ASTArithmeticOperatorNode	arithmeticOperation(ASTNode.Type operator, ASTNode2... list) Creates a new ASTArithmeticOperatorNode of type operator and adds the given nodes as children.
static int	countType(ASTNode2 node, ASTNode.Type type) Counts the number of nodes that have ASTNode.Type type in the tree rooted at node.
static ASTArithmeticOperatorNode	diff(ASTNode2... ast) Creates a new ASTArithmeticOperatorNode of type MINUS and adds the given nodes as children.
static ASTDivideNode	divideBy(ASTNode2 numerator, ASTNode2 denominator) Divides an ASTNode2 by another ASTNode2
static ASTRelationalOperatorNode	eq(ASTNode2 left, ASTNode2 right) Creates a new ASTRelationalOperatorNode of type RELATIONAL_EQ.
static ASTPowerNode	exp(ASTNode2 exponent) Returns a new ASTPowerNode that represents Euler's constant raised by the power of the given exponent.
static java.lang.String	formulaToString(ASTNode2 tree) Returns the formula from the given ASTNode2 as an SBML Level 1 text-string mathematical formula.
static ASTDivideNode	frac(ASTNode2 numerator, ASTNode2 denominator) Creates a new ASTDivideNode with the given nodes as children.
static ASTDivideNode	frac(int numerator, ASTNode2 denominator) Creates a new ASTDivideNode with the given numerator and denominator.
static ASTRelationalOperatorNode	geq(ASTNode2 left, ASTNode2 right) Creates an ASTRelationalOperatorNode representing greater or equal for the two given nodes.
static ASTRelationalOperatorNode	gt(ASTNode2 left, ASTNode2 right) Creates an ASTRelationalOperatorNode representing greater than for the two given left and right child.
static ASTRelationalOperatorNode	leq(ASTNode2 left, ASTNode2 right) Creates an ASTRelationalOperatorNode representing less or equal for the two given left and right child.
static ASTLogarithmNode	log(ASTNode2 value) Creates an ASTLogarithmNode representing a logarithm to base 10 of the given value.
static ASTLogarithmNode	log(ASTNode2 base, ASTNode2 value) Creates an ASTLogarithmNode that represents the logarithm function with the given base and value.
static ASTRelationalOperatorNode	lt(ASTNode2 left, ASTNode2 right) Creates a ASTRelationalOperatorNode that performs a less than comparison between two ASTNode2s.
static ASTRelationalOperatorNode	lt(java.lang.String variable, ASTNode2 node) Creates an ASTRelationalOperatorNode that performs a less than comparison between a variable and another ASTNode2.
static ASTMinusNode	minus(ASTNode2 node1, ASTNode2 node2) Subtracts an ASTNode2 from another ASTNode2.
static ASTMinusNode	minus(ASTNode2 node, double real) Subtracts the given number from an ASTNode2
static ASTMinusNode	minus(ASTNode2 node, int integer) Subtracts an integer number from ASTNode2.
static ASTMinusNode	minus(ASTNode2 node, int integer, java.lang.String unitsID) Subtracts an integer number from ASTNode2 and sets the units of ASTCnIntegerNode to the specified unitsID.
static ASTArithmeticOperatorNode	multiplyWith(ASTNode2... nodes) Multiplies an ASTNode2 with the given nodes, i.e., all given nodes will be children of this ASTArithmeticOperatorNode, whose type will be set to ASTNode.Type.TIMES.
static ASTTimesNode	multiplyWith(ASTNode2 node1, ASTNode2 node2) Multiplies an ASTNode2 with another ASTNode2.
static ASTRelationalOperatorNode	neq(ASTNode2 left, ASTNode2 right) Creates an ASTNode2 that performs a not equal comparison between two ASTNode2s.
static ASTLogicalOperatorNode	not(ASTNode2... ast) Creates an ASTLogicalOperatorNode of type ASTNode.Type.LOGICAL_NOT and adds the given nodes as children.
static ASTLogicalOperatorNode	or(ASTNode2... ast) Creates an ASTLogicalOperatorNode of type ASTNode.Type.LOGICAL_OR and adds the given nodes as children.
static ASTNode2	parseFormula(java.lang.String formula) Parses a text-string mathematical formula and an Abstract Syntax Tree representation.
static java.lang.String	parseMathML(java.lang.String fileName) Return String representation of specified MathML file
static ASTPiecewiseFunctionNode	piecewise(ASTQualifierNode node, ASTQualifierNode... nodes) Creates a piecewise ASTPiecewiseFunctionNode.
static ASTPlusNode	plus(ASTNode2 node1, ASTNode2 node2) Adds an ASTNode2 to an ASTNode2.
static ASTPlusNode	plus(ASTNode2 node, double real) Adds a real number to ASTNode2.
static ASTPlusNode	plus(ASTNode2 node, int integer) Adds an integer number to ASTNode2.
static ASTPowerNode	pow(ASTNode2 basis, ASTNode2 exponent) Creates a power ASTNode2.
static ASTPowerNode	pow(ASTNode2 basis, double exponent) Creates a power ASTPowerNode with an ASTNode2 basis and a real exponent.
static ASTPowerNode	pow(ASTNode2 basis, int exponent) Creates a power ASTPowerNode with an ASTNode2 basis and an integer exponent.
static ASTArithmeticOperatorNode	product(ASTNode2... ast) Creates an ASTArithmeticOperatorNode of type ASTNode.Type.PRODUCT and adds the given nodes as children.
static ASTBinaryFunctionNode	reduceToBinary(ASTFunction node) Reduces an ASTFunction to a binary tree, e.g., if the formula in the ASTFunction is and(x, y, z) then the formula of the reduced node would be and(and(x, y), z).
static ASTRelationalOperatorNode	relational(ASTNode.Type type, ASTNode2 a, ASTNode2 b) Creates a relational ASTRelationalOperatorNode of the given type with the two given children left and right.
static ASTRootNode	root(ASTNode2 rootExponent, ASTNode2 radicand) Creates a root of type ASTNode2.
static void	setParentSBMLObject(ASTNode2 node, MathContainer parent) Sets the Parent of the node and its children to the given value
static ASTRootNode	sqrt(ASTNode2 radicand) Creates a square root of type ASTRootNode with the specified radicand of type ASTNode2.
static ASTArithmeticOperatorNode	sum(ASTNode2... ast) Creates an ASTArithmeticOperatorNode of type ASTNode.Type.SUM and adds the given nodes as children.
static ASTTimesNode	times(ASTNode2 node1, ASTNode2 node2) Creates a new ASTTimesNode with exactly two children
static ASTTimesNode	times(ASTNode2 node1, double real) Adds a real number to ASTNode2
static ASTTimesNode	times(ASTNode2 node1, int integer) Adds an integer to ASTNode2
static ASTNode2	toASTNode2(ASTNode astNode)
static ASTMinusNode	uMinus(ASTNode2 ast) Creates a new ASTMinusNode that has exactly one child and which is of type ASTNode.Type.MINUS, i.e., this negates what is encoded in ast.
static ASTLogicalOperatorNode	xor(ASTNode2... ast) Creates an ASTLogicalOperatorNode of type ASTNode.Type.LOGICAL_XOR and adds the given nodes as children.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ASTFactory

public ASTFactory()

Method Detail

and

public static ASTLogicalOperatorNode and(ASTNode2... ast)

Creates an ASTLogicalOperatorNode of type ASTNode.Type.LOGICAL_AND and adds the given nodes as children.

Parameters:

ast -

Returns:

an ASTLogicalOperatorNode with the given nodes as children.

arithmeticOperation

public static ASTArithmeticOperatorNode arithmeticOperation(ASTNode.Type operator,
                                                            ASTNode2... list)

Creates a new ASTArithmeticOperatorNode of type operator and adds the given nodes as children.

Parameters:

operator - the type of arithmetic operation

list - the children of the new ASTNode2

Returns:

a new ASTNode2 of type operator and adds the given nodes as children.

countType

public static int countType(ASTNode2 node,
                            ASTNode.Type type)

Counts the number of nodes that have ASTNode.Type type in the tree rooted at node.

Parameters:

node - ASTNode2

type - ASTNode.Type

Returns:

int

diff

public static ASTArithmeticOperatorNode diff(ASTNode2... ast)

Creates a new ASTArithmeticOperatorNode of type MINUS and adds the given nodes as children. Resulting abstract syntax tree will be reduced to binary form.

Parameters:

ast - the children of the new ASTNode

Returns:

a new ASTArithmeticOperatorNode of type MINUS and adds the given nodes as children

divideBy

public static ASTDivideNode divideBy(ASTNode2 numerator,
                                     ASTNode2 denominator)

Divides an ASTNode2 by another ASTNode2

Parameters:

numerator - ASTNode2

denominator - ASTNode2

Returns:

node ASTDivideNode

eq

public static ASTRelationalOperatorNode eq(ASTNode2 left,
                                           ASTNode2 right)

Creates a new ASTRelationalOperatorNode of type RELATIONAL_EQ.

Parameters:

left - the left child.

right - the right child.

Returns:

a new ASTRelationalOperatorNode of type RELATIONAL_EQ.

exp

public static ASTPowerNode exp(ASTNode2 exponent)

Returns a new ASTPowerNode that represents Euler's constant raised by the power of the given exponent.

Parameters:

exponent - the exponent

Returns:

a new ASTPowerNode that represents Euler's constant raised by the power of the given exponent.

formulaToString

public static java.lang.String formulaToString(ASTNode2 tree)
                                        throws SBMLException

Returns the formula from the given ASTNode2 as an SBML Level 1 text-string mathematical formula.

Parameters:

tree - the root of the ASTNode2 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

frac

public static ASTDivideNode frac(ASTNode2 numerator,
                                 ASTNode2 denominator)

Creates a new ASTDivideNode with the given nodes as children.

Parameters:

numerator - the numerator ASTNode2

denominator - the denominator ASTNode2

Returns:

a new ASTDivideNode with the given nodes as children.

frac

public static ASTDivideNode frac(int numerator,
                                 ASTNode2 denominator)

Creates a new ASTDivideNode with the given numerator and denominator.

Parameters:

numerator - the integer numerator

denominator - the denominator ASTNode2

Returns:

a new ASTDivideNode with the given numerator and denominator.

geq

public static ASTRelationalOperatorNode geq(ASTNode2 left,
                                            ASTNode2 right)

Creates an ASTRelationalOperatorNode representing greater or equal for the two given nodes.

Parameters:

left - the left child.

right - the right child.

Returns:

an ASTRelationalOperatorNode representing greater or equal.

gt

public static ASTRelationalOperatorNode gt(ASTNode2 left,
                                           ASTNode2 right)

Creates an ASTRelationalOperatorNode representing greater than for the two given left and right child.

Parameters:

left - the left child.

right - the right child.

Returns:

an ASTRelationalOperatorNode representing greater than for the two given left and right child.

leq

public static ASTRelationalOperatorNode leq(ASTNode2 left,
                                            ASTNode2 right)

Creates an ASTRelationalOperatorNode representing less or equal for the two given left and right child.

Parameters:

left - the left child.

right - the right child.

Returns:

an ASTRelationalOperatorNode representing less or equal for the two given left and right child.

log

public static ASTLogarithmNode log(ASTNode2 value)

Creates an ASTLogarithmNode representing a logarithm to base 10 of the given value.

Parameters:

value - the value which is the argument of the logarithm.

Returns:

an ASTLogarithmNode representing a logarithm to base 10 of the given value.

log

public static ASTLogarithmNode log(ASTNode2 base,
                                   ASTNode2 value)

Creates an ASTLogarithmNode that represents the logarithm function with the given base and value. The parent SBML object will be taken from the ASTNode2 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 ASTLogarithmNode 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 ASTRelationalOperatorNode lt(ASTNode2 left,
                                           ASTNode2 right)

Creates a ASTRelationalOperatorNode that performs a less than comparison between two ASTNode2s. 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 ASTRelationalOperatorNode that performs a less than comparison between two ASTNode2s.

lt

public static ASTRelationalOperatorNode lt(java.lang.String variable,
                                           ASTNode2 node)

Creates an ASTRelationalOperatorNode that performs a less than comparison between a variable and another ASTNode2. The parent SBML object will be taken from the given ASTNode2.

Parameters:

variable - the left child.

node - the right child.

Returns:

an ASTRelationalOperatorNode that performs a less than comparison between a variable and another ASTNode2.

minus

public static ASTMinusNode minus(ASTNode2 node1,
                                 ASTNode2 node2)

Subtracts an ASTNode2 from another ASTNode2.

Parameters:

node1 - ASTNode2

node2 - ASTNode2

Returns:

minus ASTMinusNode

minus

public static ASTMinusNode minus(ASTNode2 node,
                                 double real)

Subtracts the given number from an ASTNode2

Parameters:

node - ASTNode2

real - double value

Returns:

minus ASTMinusNode

minus

public static ASTMinusNode minus(ASTNode2 node,
                                 int integer)

Subtracts an integer number from ASTNode2.

Parameters:

node - ASTNode2

integer - int

Returns:

minus ASTMinusNode

minus

public static ASTMinusNode minus(ASTNode2 node,
                                 int integer,
                                 java.lang.String unitsID)

Subtracts an integer number from ASTNode2 and sets the units of ASTCnIntegerNode to the specified unitsID.

Parameters:

node - ASTNode2

integer - int

unitsID - String

Returns:

minus ASTMinusNode

multiplyWith

public static ASTArithmeticOperatorNode multiplyWith(ASTNode2... nodes)

Multiplies an ASTNode2 with the given nodes, i.e., all given nodes will be children of this ASTArithmeticOperatorNode, whose type will be set to ASTNode.Type.TIMES. Resulting abstract syntax tree will be reduced to binary form.

Parameters:

nodes - some ASTNode2

Returns:

times ASTArithmeticOperatorNode

multiplyWith

public static ASTTimesNode multiplyWith(ASTNode2 node1,
                                        ASTNode2 node2)

Multiplies an ASTNode2 with another ASTNode2.

Parameters:

node1 - ASTNode2

node2 - ASTNode2

Returns:

times ASTTimesNode

neq

public static ASTRelationalOperatorNode neq(ASTNode2 left,
                                            ASTNode2 right)

Creates an ASTNode2 that performs a not equal comparison between two ASTNode2s.

Parameters:

left - the left child.

right - the right child.

Returns:

an ASTRelationalOperatorNode that performs a not equal comparison between two ASTNode2s.

not

public static ASTLogicalOperatorNode not(ASTNode2... ast)

Creates an ASTLogicalOperatorNode of type ASTNode.Type.LOGICAL_NOT and adds the given nodes as children.

Parameters:

ast -

Returns:

an ASTLogicalOperatorNode with the given nodes as children.

or

public static ASTLogicalOperatorNode or(ASTNode2... ast)

Creates an ASTLogicalOperatorNode of type ASTNode.Type.LOGICAL_OR and adds the given nodes as children.

Parameters:

ast -

Returns:

an ASTLogicalOperatorNode with the given nodes as children.

parseFormula

public static ASTNode2 parseFormula(java.lang.String formula)
                             throws ParseException

Parses a text-string mathematical formula and an Abstract Syntax Tree representation.

Parameters:

formula - a text-string mathematical formula.

Returns:

an ASTNode2 representing the formula.

Throws:

ParseException - If the given formula is not of valid format or cannot be parsed for other reasons.

parseMathML

public static java.lang.String parseMathML(java.lang.String fileName)

Return String representation of specified MathML file

Parameters:

fileName -

Returns:

contents

piecewise

public static ASTPiecewiseFunctionNode piecewise(ASTQualifierNode node,
                                                 ASTQualifierNode... nodes)

Creates a piecewise ASTPiecewiseFunctionNode.

At least one ASTQualifierNode must be given as a child. The parent SBML object of this first node will be the parent of the resulting ASTPiecewiseFunctionNode.

Parameters:

node - the parent SBML object of this node will be the parent of the resulting ASTPiecewiseFunctionNode.

nodes - the children of the new piecewise ASTNode2

Returns:

a piecewise ASTPiecewiseFunctionNode.

plus

public static ASTPlusNode plus(ASTNode2 node1,
                               ASTNode2 node2)

Adds an ASTNode2 to an ASTNode2.

Parameters:

node1 - ASTNode2

node2 - ASTNode2

Returns:

plus ASTArithmeticOperatorNode

plus

public static ASTPlusNode plus(ASTNode2 node,
                               double real)

Adds a real number to ASTNode2.

Parameters:

node - ASTNode2

real - double value

Returns:

plus ASTPlusNode

plus

public static ASTPlusNode plus(ASTNode2 node,
                               int integer)

Adds an integer number to ASTNode2.

Parameters:

node - ASTNode2

integer - int

Returns:

plus ASTPlusNode

pow

public static ASTPowerNode pow(ASTNode2 basis,
                               ASTNode2 exponent)

Creates a power ASTNode2.

Parameters:

basis - the basis

exponent - the exponent

Returns:

a power ASTPowerNode.

pow

public static ASTPowerNode pow(ASTNode2 basis,
                               double exponent)

Creates a power ASTPowerNode with an ASTNode2 basis and a real exponent.

Parameters:

basis - the basis

exponent - the exponent

Returns:

a power ASTPowerNode.

pow

public static ASTPowerNode pow(ASTNode2 basis,
                               int exponent)

Creates a power ASTPowerNode with an ASTNode2 basis and an integer exponent.

Parameters:

basis - the basis

exponent - the exponent

Returns:

a power ASTPowerNode.

product

public static ASTArithmeticOperatorNode product(ASTNode2... ast)

Creates an ASTArithmeticOperatorNode of type ASTNode.Type.PRODUCT and adds the given nodes as children.

Parameters:

ast -

Returns:

an ASTArithmeticOperatorNode with the given nodes as children.

reduceToBinary

public static ASTBinaryFunctionNode reduceToBinary(ASTFunction node)

Reduces an ASTFunction to a binary tree, e.g., if the formula in the ASTFunction is and(x, y, z) then the formula of the reduced node would be and(and(x, y), z).

Parameters:

node - ASTFunction

Returns:

binaryNode ASTBinaryFunctionNode

relational

public static ASTRelationalOperatorNode relational(ASTNode.Type type,
                                                   ASTNode2 a,
                                                   ASTNode2 b)

Creates a relational ASTRelationalOperatorNode 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.

a - the left child.

b - the right child.

Returns:

a relational ASTRelationalOperatorNode of the given type with the two given children left and right.

root

public static ASTRootNode root(ASTNode2 rootExponent,
                               ASTNode2 radicand)

Creates a root of type ASTNode2.

Parameters:

radicand - the radicand ASTNode2

rootExponent - the exponent of the root element ASTNode2

Returns:

a root of type ASTRootNode.

setParentSBMLObject

public static void setParentSBMLObject(ASTNode2 node,
                                       MathContainer parent)

Sets the Parent of the node and its children to the given value

Parameters:

node - the orphan node

parent - the parent

sqrt

public static ASTRootNode sqrt(ASTNode2 radicand)

Creates a square root of type ASTRootNode with the specified radicand of type ASTNode2.

Parameters:

radicand - ASTNode2

Returns:

a root ASTRootNode.

sum

public static ASTArithmeticOperatorNode sum(ASTNode2... ast)

Creates an ASTArithmeticOperatorNode of type ASTNode.Type.SUM and adds the given nodes as children.

Parameters:

ast -

Returns:

an ASTArithmeticOperatorNode with the given nodes as children.

times

public static ASTTimesNode times(ASTNode2 node1,
                                 ASTNode2 node2)

Creates a new ASTTimesNode with exactly two children

Parameters:

node1 - ASTNode2

node2 - ASTNode2

Returns:

a new ASTTimesNode that has exactly two children

times

public static ASTTimesNode times(ASTNode2 node1,
                                 double real)

Adds a real number to ASTNode2

Parameters:

node1 - ASTNode2

real - double

Returns:

a new ASTTimesNode that has exactly two children

times

public static ASTTimesNode times(ASTNode2 node1,
                                 int integer)

Adds an integer to ASTNode2

Parameters:

node1 - ASTNode2

integer - int

Returns:

a new ASTTimesNode that has exactly two children

toASTNode2

public static ASTNode2 toASTNode2(ASTNode astNode)

Parameters:

astNode -

Returns:

uMinus

public static ASTMinusNode uMinus(ASTNode2 ast)

Creates a new ASTMinusNode that has exactly one child and which is of type ASTNode.Type.MINUS, i.e., this negates what is encoded in ast.

Parameters:

ast - ASTNode2

Returns:

a new ASTMinusNode that has exactly one child and which is of type minus, i.e., this negates what is encoded in ast.

xor

public static ASTLogicalOperatorNode xor(ASTNode2... ast)

Creates an ASTLogicalOperatorNode of type ASTNode.Type.LOGICAL_XOR and adds the given nodes as children.

Parameters:

ast -

Returns:

an ASTLogicalOperatorNode with the given nodes as children.