org.sbml.jsbml.math.compiler

Interface AbstractASTNodeCompiler

public interface AbstractASTNodeCompiler

A compiler for abstract syntax trees. This compiler evaluates the values represented by ASTNode2s. It defines how to perform mathematical or other operations on these data types. Recursion can be performed as follows:

   public ASTNodeValue doSomeThing(AbstractASTNode ast) {
     ...
     ASTNodeValue child = ast.compile(this);
     ...
     return new ASTNodeValue(doSomeThing(child), this);
   }
 

Since:

1.0

Version:

$Rev: 1818 $

Author:

Andreas Dräger, Victor Kofia

Method Summary

Methods

Modifier and Type	Method and Description
ASTNodeValue	abs(AbstractASTNode value) The absolute value represented by the given AbstractASTNode.
ASTNodeValue	and(java.util.List<AbstractASTNode> values)
ASTNodeValue	arccos(AbstractASTNode value)
ASTNodeValue	arccosh(AbstractASTNode value)
ASTNodeValue	arccot(AbstractASTNode value)
ASTNodeValue	arccoth(AbstractASTNode value)
ASTNodeValue	arccsc(AbstractASTNode value)
ASTNodeValue	arccsch(AbstractASTNode value)
ASTNodeValue	arcsec(AbstractASTNode value)
ASTNodeValue	arcsech(AbstractASTNode value)
ASTNodeValue	arcsin(AbstractASTNode value)
ASTNodeValue	arcsinh(AbstractASTNode value)
ASTNodeValue	arctan(AbstractASTNode value)
ASTNodeValue	arctanh(AbstractASTNode value)
ASTNodeValue	ceiling(AbstractASTNode value)
ASTNodeValue	compile(AbstractASTNode node)
ASTNodeValue	compile(CallableSBase variable)
ASTNodeValue	compile(Compartment c)
ASTNodeValue	compile(double mantissa, int exponent, java.lang.String units) Creates an ASTNodeValue that represents a real number in scientific notation, i.e., mantissa * 10^exponent, and the given units.
ASTNodeValue	compile(double real, java.lang.String units)
ASTNodeValue	compile(int integer, java.lang.String units)
ASTNodeValue	compile(java.lang.String name) A compiler will also have to deal with a name.
ASTNodeValue	cos(AbstractASTNode value)
ASTNodeValue	cosh(AbstractASTNode value)
ASTNodeValue	cot(AbstractASTNode value)
ASTNodeValue	coth(AbstractASTNode value)
ASTNodeValue	csc(AbstractASTNode value)
ASTNodeValue	csch(AbstractASTNode value)
ASTNodeValue	delay(java.lang.String delayName, AbstractASTNode x, AbstractASTNode delay, java.lang.String timeUnits) Evaluates delay functions.
ASTNodeValue	eq(AbstractASTNode left, AbstractASTNode right) Equal.
ASTNodeValue	exp(AbstractASTNode value)
ASTNodeValue	factorial(AbstractASTNode value)
ASTNodeValue	floor(AbstractASTNode value)
ASTNodeValue	frac(AbstractASTNode numerator, AbstractASTNode denominator) Fraction of two AbstractASTNodes
ASTNodeValue	frac(int numerator, int denominator) A fraction of two int values.
ASTNodeValue	function(FunctionDefinition functionDefinition, java.util.List<AbstractASTNode> args)
ASTNodeValue	function(java.lang.String functionDefinitionName, java.util.List<AbstractASTNode> args)
ASTNodeValue	geq(AbstractASTNode left, AbstractASTNode right) Greater equal.
ASTNodeValue	getConstantAvogadro(java.lang.String name) Creates an ASTNodeValue that represent's Avogadro's number.
ASTNodeValue	getConstantE()
ASTNodeValue	getConstantFalse()
ASTNodeValue	getConstantPi()
ASTNodeValue	getConstantTrue()
ASTNodeValue	getNegativeInfinity()
ASTNodeValue	getPositiveInfinity()
ASTNodeValue	gt(AbstractASTNode left, AbstractASTNode right) Greater than.
ASTNodeValue	lambda(java.util.List<AbstractASTNode> values) The body of a FunctionDefinition.
ASTNodeValue	leq(AbstractASTNode left, AbstractASTNode right) Less equal.
ASTNodeValue	ln(AbstractASTNode value) Natural logarithm.
ASTNodeValue	log(AbstractASTNode value) Logarithm of the given value to base 10.
ASTNodeValue	log(AbstractASTNode base, AbstractASTNode value) Logarithm of the given value to the given base.
ASTNodeValue	lt(AbstractASTNode left, AbstractASTNode right) Less than.
ASTNodeValue	minus(java.util.List<AbstractASTNode> values) Subtraction.
ASTNodeValue	neq(AbstractASTNode left, AbstractASTNode right) Not equal.
ASTNodeValue	not(AbstractASTNode value)
ASTNodeValue	or(java.util.List<AbstractASTNode> values)
ASTNodeValue	piecewise(java.util.List<AbstractASTNode> values)
ASTNodeValue	plus(java.util.List<AbstractASTNode> values)
ASTNodeValue	pow(AbstractASTNode base, AbstractASTNode exponent)
ASTNodeValue	root(AbstractASTNode rootExponent, AbstractASTNode radiant)
ASTNodeValue	root(double rootExponent, AbstractASTNode radiant)
ASTNodeValue	sec(AbstractASTNode value)
ASTNodeValue	sech(AbstractASTNode value)
ASTNodeValue	selector(java.util.List<AbstractASTNode> nodes)
ASTNodeValue	sin(AbstractASTNode value)
ASTNodeValue	sinh(AbstractASTNode value)
ASTNodeValue	sqrt(AbstractASTNode radiant) Square root.
ASTNodeValue	symbolTime(java.lang.String time) The simulation time.
ASTNodeValue	tan(AbstractASTNode value)
ASTNodeValue	tanh(AbstractASTNode value)
ASTNodeValue	times(java.util.List<AbstractASTNode> values) Product of all given AbstractASTNodes.
ASTNodeValue	uMinus(AbstractASTNode value) Unary minus, i.e., negation of the given AbstractASTNode.
ASTNodeValue	unknownValue() Dealing with a malformed AbstractASTNode.
ASTNodeValue	vector(java.util.List<AbstractASTNode> nodes) Dealing with a vector.
ASTNodeValue	xor(java.util.List<AbstractASTNode> values) Exclusive or.

Method Detail

abs

ASTNodeValue abs(AbstractASTNode value)
                 throws SBMLException

The absolute value represented by the given AbstractASTNode.

Parameters:

value - Must be interpretable as a Number.

Returns:

Throws:

SBMLException

and

ASTNodeValue and(java.util.List<AbstractASTNode> values)
                 throws SBMLException

Parameters:

values -

Returns:

Throws:

SBMLException

arccos

ASTNodeValue arccos(AbstractASTNode value)
                    throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arccosh

ASTNodeValue arccosh(AbstractASTNode value)
                     throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arccot

ASTNodeValue arccot(AbstractASTNode value)
                    throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arccoth

ASTNodeValue arccoth(AbstractASTNode value)
                     throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arccsc

ASTNodeValue arccsc(AbstractASTNode value)
                    throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arccsch

ASTNodeValue arccsch(AbstractASTNode value)
                     throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arcsec

ASTNodeValue arcsec(AbstractASTNode value)
                    throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arcsech

ASTNodeValue arcsech(AbstractASTNode value)
                     throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arcsin

ASTNodeValue arcsin(AbstractASTNode value)
                    throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arcsinh

ASTNodeValue arcsinh(AbstractASTNode value)
                     throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arctan

ASTNodeValue arctan(AbstractASTNode value)
                    throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arctanh

ASTNodeValue arctanh(AbstractASTNode value)
                     throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

ceiling

ASTNodeValue ceiling(AbstractASTNode value)
                     throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

compile

ASTNodeValue compile(Compartment c)

Parameters:

c -

Returns:

compile

ASTNodeValue compile(double mantissa,
                   int exponent,
                   java.lang.String units)

Creates an ASTNodeValue that represents a real number in scientific notation, i.e., mantissa * 10^exponent, and the given units.

Parameters:

mantissa - The number to be multiplied with ten to the power of the given exponent.

exponent - The exponent for the multiplier ten.

units - The identifier of the units object associated with the number represented by this element. Can be null if no units have been defined.

Returns:

compile

ASTNodeValue compile(double real,
                   java.lang.String units)

Parameters:

real -

units - A String representing the Unit of the given number. This can be the identifier of a UnitDefinition in the model or a literal in Unit.Kind. Can be null if no units have been defined.

Returns:

compile

ASTNodeValue compile(int integer,
                   java.lang.String units)

Parameters:

integer -

units - A String representing the Unit of the given number. This can be the identifier of a UnitDefinition in the model or a literal in Unit.Kind. Can be null if no units have been defined.

Returns:

compile

ASTNodeValue compile(CallableSBase variable)
                     throws SBMLException

Parameters:

variable -

Returns:

Throws:

SBMLException

compile

ASTNodeValue compile(AbstractASTNode node)

Parameters:

node -

Returns:

compile

ASTNodeValue compile(java.lang.String name)

A compiler will also have to deal with a name. The meaning of this can be various. For instance, the name may refer to a Species in the system. In case of numerical computation, the ASTNodeCompiler must create an ASTNodeValue representing the current value of this Species.

Parameters:

name -

Returns:

cos

ASTNodeValue cos(AbstractASTNode value)
                 throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

cosh

ASTNodeValue cosh(AbstractASTNode value)
                  throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

cot

ASTNodeValue cot(AbstractASTNode value)
                 throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

coth

ASTNodeValue coth(AbstractASTNode value)
                  throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

csc

ASTNodeValue csc(AbstractASTNode value)
                 throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

csch

ASTNodeValue csch(AbstractASTNode value)
                  throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

delay

ASTNodeValue delay(java.lang.String delayName,
                 AbstractASTNode x,
                 AbstractASTNode delay,
                 java.lang.String timeUnits)
                   throws SBMLException

Evaluates delay functions.

Parameters:

delayName - the name of this delay function.

x -

delay - an expression of a positive duration time (the amoutn of delay)

timeUnits - the units for the delay.

Returns:

Throws:

SBMLException

eq

ASTNodeValue eq(AbstractASTNode left,
              AbstractASTNode right)
                throws SBMLException

Equal.

Parameters:

left -

right -

Returns:

Throws:

SBMLException

exp

ASTNodeValue exp(AbstractASTNode value)
                 throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

factorial

ASTNodeValue factorial(AbstractASTNode value)
                       throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

floor

ASTNodeValue floor(AbstractASTNode value)
                   throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

frac

ASTNodeValue frac(AbstractASTNode numerator,
                AbstractASTNode denominator)
                  throws SBMLException

Fraction of two AbstractASTNodes

Parameters:

numerator -

denominator -

Returns:

Throws:

SBMLException

frac

ASTNodeValue frac(int numerator,
                int denominator)
                  throws SBMLException

A fraction of two int values.

Parameters:

numerator -

denominator -

Returns:

Throws:

SBMLException

function

ASTNodeValue function(FunctionDefinition functionDefinition,
                    java.util.List<AbstractASTNode> args)
                      throws SBMLException

Parameters:

functionDefinition -

args - Values to be inserted into the parameter list of the function.

Returns:

Throws:

SBMLException

function

ASTNodeValue function(java.lang.String functionDefinitionName,
                    java.util.List<AbstractASTNode> args)
                      throws SBMLException

Parameters:

functionDefinition - name

args - Values to be inserted into the parameter list of the function.

Returns:

Throws:

SBMLException

geq

ASTNodeValue geq(AbstractASTNode left,
               AbstractASTNode right)
                 throws SBMLException

Greater equal.

Parameters:

left -

right -

Returns:

Throws:

SBMLException

getConstantAvogadro

ASTNodeValue getConstantAvogadro(java.lang.String name)

Creates an ASTNodeValue that represent's Avogadro's number. Optionally, the compiler may associate the given name with this number.

Parameters:

name - An optional name for Avogadro's number.

Returns:

getConstantE

ASTNodeValue getConstantE()

Returns:

getConstantFalse

ASTNodeValue getConstantFalse()

Returns:

getConstantPi

ASTNodeValue getConstantPi()

Returns:

getConstantTrue

ASTNodeValue getConstantTrue()

Returns:

getNegativeInfinity

ASTNodeValue getNegativeInfinity()
                                 throws SBMLException

Returns:

Throws:

SBMLException

getPositiveInfinity

ASTNodeValue getPositiveInfinity()

Returns:

gt

ASTNodeValue gt(AbstractASTNode left,
              AbstractASTNode right)
                throws SBMLException

Greater than.

Parameters:

left -

right -

Returns:

Throws:

SBMLException

lambda

ASTNodeValue lambda(java.util.List<AbstractASTNode> values)
                    throws SBMLException

The body of a FunctionDefinition.

Parameters:

values - Place holders for arguments.

Returns:

Throws:

SBMLException

leq

ASTNodeValue leq(AbstractASTNode left,
               AbstractASTNode right)
                 throws SBMLException

Less equal.

Parameters:

left -

right -

Returns:

Throws:

SBMLException

ln

ASTNodeValue ln(AbstractASTNode value)
                throws SBMLException

Natural logarithm.

Parameters:

value -

Returns:

Throws:

SBMLException

log

ASTNodeValue log(AbstractASTNode value)
                 throws SBMLException

Logarithm of the given value to base 10.

Parameters:

value -

Returns:

Throws:

SBMLException

log

ASTNodeValue log(AbstractASTNode base,
               AbstractASTNode value)
                 throws SBMLException

Logarithm of the given value to the given base.

Parameters:

base -

value -

Returns:

Throws:

SBMLException

lt

ASTNodeValue lt(AbstractASTNode left,
              AbstractASTNode right)
                throws SBMLException

Less than.

Parameters:

left -

right -

Returns:

Throws:

SBMLException

minus

ASTNodeValue minus(java.util.List<AbstractASTNode> values)
                   throws SBMLException

Subtraction.

Parameters:

values -

Returns:

Throws:

SBMLException

neq

ASTNodeValue neq(AbstractASTNode left,
               AbstractASTNode right)
                 throws SBMLException

Not equal.

Parameters:

left -

right -

Returns:

Throws:

SBMLException

not

ASTNodeValue not(AbstractASTNode value)
                 throws SBMLException

Parameters:

value - This value must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

or

ASTNodeValue or(java.util.List<AbstractASTNode> values)
                throws SBMLException

Parameters:

values - These values must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

piecewise

ASTNodeValue piecewise(java.util.List<AbstractASTNode> values)
                       throws SBMLException

Parameters:

values -

Returns:

Throws:

SBMLException

plus

ASTNodeValue plus(java.util.List<AbstractASTNode> values)
                  throws SBMLException

Parameters:

values -

Returns:

Throws:

SBMLException

pow

ASTNodeValue pow(AbstractASTNode base,
               AbstractASTNode exponent)
                 throws SBMLException

Parameters:

base -

exponent -

Returns:

Throws:

SBMLException

root

ASTNodeValue root(AbstractASTNode rootExponent,
                AbstractASTNode radiant)
                  throws SBMLException

Parameters:

rootExponent -

radiant -

Returns:

Throws:

SBMLException

root

ASTNodeValue root(double rootExponent,
                AbstractASTNode radiant)
                  throws SBMLException

Parameters:

rootExponent -

radiant -

Returns:

Throws:

SBMLException

sec

ASTNodeValue sec(AbstractASTNode value)
                 throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

sech

ASTNodeValue sech(AbstractASTNode value)
                  throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

selector

ASTNodeValue selector(java.util.List<AbstractASTNode> nodes)
                      throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

sin

ASTNodeValue sin(AbstractASTNode value)
                 throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

sinh

ASTNodeValue sinh(AbstractASTNode value)
                  throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

sqrt

ASTNodeValue sqrt(AbstractASTNode radiant)
                  throws SBMLException

Square root.

Parameters:

radiant - This value must be interpretable as a Number.

Returns:

Throws:

SBMLException

symbolTime

ASTNodeValue symbolTime(java.lang.String time)

The simulation time.

Parameters:

time - The name of the time symbol.

Returns:

An ASTNodeValue that represents the current time.

tan

ASTNodeValue tan(AbstractASTNode value)
                 throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

tanh

ASTNodeValue tanh(AbstractASTNode value)
                  throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

times

ASTNodeValue times(java.util.List<AbstractASTNode> values)
                   throws SBMLException

Product of all given AbstractASTNodes.

Parameters:

values - These values must be interpretable to Number.

Returns:

Throws:

SBMLException

uMinus

ASTNodeValue uMinus(AbstractASTNode value)
                    throws SBMLException

Unary minus, i.e., negation of the given AbstractASTNode.

Parameters:

value -

Returns:

Throws:

SBMLException

unknownValue

ASTNodeValue unknownValue()
                          throws SBMLException

Dealing with a malformed AbstractASTNode.

Returns:

Throws:

SBMLException

vector

ASTNodeValue vector(java.util.List<AbstractASTNode> nodes)
                    throws SBMLException

Dealing with a vector.

Returns:

Throws:

SBMLException

xor

ASTNodeValue xor(java.util.List<AbstractASTNode> values)
                 throws SBMLException

Exclusive or.

Parameters:

values - It must be possible to evaluate the given values to Boolean.

Returns:

Throws:

SBMLException