org.sbml.jsbml.util.compilers

Interface ASTNodeCompiler

All Known Implementing Classes:

FindUnitsCompiler, FormulaCompiler, FormulaCompilerLibSBML, FormulaCompilerNoPiecewise, HTMLFormula, LaTeXCompiler, LibSBMLFormulaCompiler, MathMLCompiler, UnitsCompiler

public interface ASTNodeCompiler

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

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

Since:

0.8

Version:

$Rev$

Author:

Andreas Dräger

Method Summary

Modifier and Type	Method and Description
ASTNodeValue	abs(ASTNode value) The absolute value represented by the given ASTNode.
ASTNodeValue	and(java.util.List<ASTNode> values)
ASTNodeValue	arccos(ASTNode value)
ASTNodeValue	arccosh(ASTNode value)
ASTNodeValue	arccot(ASTNode value)
ASTNodeValue	arccoth(ASTNode value)
ASTNodeValue	arccsc(ASTNode value)
ASTNodeValue	arccsch(ASTNode value)
ASTNodeValue	arcsec(ASTNode value)
ASTNodeValue	arcsech(ASTNode value)
ASTNodeValue	arcsin(ASTNode value)
ASTNodeValue	arcsinh(ASTNode value)
ASTNodeValue	arctan(ASTNode value)
ASTNodeValue	arctanh(ASTNode value)
ASTNodeValue	ceiling(ASTNode value)
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(ASTNode value)
ASTNodeValue	cosh(ASTNode value)
ASTNodeValue	cot(ASTNode value)
ASTNodeValue	coth(ASTNode value)
ASTNodeValue	csc(ASTNode value)
ASTNodeValue	csch(ASTNode value)
ASTNodeValue	delay(java.lang.String delayName, ASTNode x, ASTNode delay, java.lang.String timeUnits) Evaluates delay functions.
ASTNodeValue	eq(ASTNode left, ASTNode right) Equal.
ASTNodeValue	exp(ASTNode value)
ASTNodeValue	factorial(ASTNode value)
ASTNodeValue	floor(ASTNode value)
ASTNodeValue	frac(ASTNode numerator, ASTNode denominator) Fraction of two ASTNodes
ASTNodeValue	frac(int numerator, int denominator) A fraction of two int values.
ASTNodeValue	function(FunctionDefinition functionDefinition, java.util.List<ASTNode> args)
ASTNodeValue	function(java.lang.String functionDefinitionName, java.util.List<ASTNode> args)
ASTNodeValue	geq(ASTNode left, ASTNode 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	getRateOf(java.lang.String name)
ASTNodeValue	gt(ASTNode left, ASTNode right) Greater than.
ASTNodeValue	implies(java.util.List<ASTNode> values) Returns the logical implies between two ASTNode.
ASTNodeValue	lambda(java.util.List<ASTNode> values) The body of a FunctionDefinition.
ASTNodeValue	leq(ASTNode left, ASTNode right) Less equal.
ASTNodeValue	ln(ASTNode value) Natural logarithm.
ASTNodeValue	log(ASTNode value) Logarithm of the given value to base 10.
ASTNodeValue	log(ASTNode base, ASTNode value) Logarithm of the given value to the given base.
ASTNodeValue	lt(ASTNode left, ASTNode right) Less than.
ASTNodeValue	max(java.util.List<ASTNode> values) Returns the maximum of the values.
ASTNodeValue	min(java.util.List<ASTNode> values) Returns the minimum of the values.
ASTNodeValue	minus(java.util.List<ASTNode> values) Subtraction.
ASTNodeValue	neq(ASTNode left, ASTNode right) Not equal.
ASTNodeValue	not(ASTNode value)
ASTNodeValue	or(java.util.List<ASTNode> values)
ASTNodeValue	piecewise(java.util.List<ASTNode> values)
ASTNodeValue	plus(java.util.List<ASTNode> values)
ASTNodeValue	pow(ASTNode base, ASTNode exponent)
ASTNodeValue	quotient(java.util.List<ASTNode> values) Returns the quotient of the division of the values.
ASTNodeValue	rem(java.util.List<ASTNode> values) Returns the remainder of the division of the values.
ASTNodeValue	root(ASTNode rootExponent, ASTNode radiant)
ASTNodeValue	root(double rootExponent, ASTNode radiant)
ASTNodeValue	sec(ASTNode value)
ASTNodeValue	sech(ASTNode value)
ASTNodeValue	selector(java.util.List<ASTNode> nodes)
ASTNodeValue	sin(ASTNode value)
ASTNodeValue	sinh(ASTNode value)
ASTNodeValue	sqrt(ASTNode radiant) Square root.
ASTNodeValue	symbolTime(java.lang.String time) The simulation time.
ASTNodeValue	tan(ASTNode value)
ASTNodeValue	tanh(ASTNode value)
ASTNodeValue	times(java.util.List<ASTNode> values) Product of all given ASTNodes.
ASTNodeValue	uMinus(ASTNode value) Unary minus, i.e., negation of the given ASTNode.
ASTNodeValue	unknownValue() Dealing with a malformed ASTNode.
ASTNodeValue	vector(java.util.List<ASTNode> nodes) Dealing with a vector.
ASTNodeValue	xor(java.util.List<ASTNode> values) Exclusive or.

Method Detail

abs

ASTNodeValue abs(ASTNode value)
          throws SBMLException

The absolute value represented by the given ASTNode.

Parameters:

value - Must be interpretable as a Number.

Returns:

Throws:

SBMLException

and

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

Parameters:

values -

Returns:

Throws:

SBMLException

arccos

ASTNodeValue arccos(ASTNode value)
             throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arccosh

ASTNodeValue arccosh(ASTNode value)
              throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arccot

ASTNodeValue arccot(ASTNode value)
             throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arccoth

ASTNodeValue arccoth(ASTNode value)
              throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arccsc

ASTNodeValue arccsc(ASTNode value)
             throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arccsch

ASTNodeValue arccsch(ASTNode value)
              throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arcsec

ASTNodeValue arcsec(ASTNode value)
             throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arcsech

ASTNodeValue arcsech(ASTNode value)
              throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arcsin

ASTNodeValue arcsin(ASTNode value)
             throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arcsinh

ASTNodeValue arcsinh(ASTNode value)
              throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arctan

ASTNodeValue arctan(ASTNode value)
             throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

arctanh

ASTNodeValue arctanh(ASTNode value)
              throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

ceiling

ASTNodeValue ceiling(ASTNode 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 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 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(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(ASTNode value)
          throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

cosh

ASTNodeValue cosh(ASTNode value)
           throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

cot

ASTNodeValue cot(ASTNode value)
          throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

coth

ASTNodeValue coth(ASTNode value)
           throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

csc

ASTNodeValue csc(ASTNode value)
          throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

csch

ASTNodeValue csch(ASTNode value)
           throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

delay

ASTNodeValue delay(java.lang.String delayName,
                   ASTNode x,
                   ASTNode 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(ASTNode left,
                ASTNode right)
         throws SBMLException

Equal.

Parameters:

left -

right -

Returns:

Throws:

SBMLException

exp

ASTNodeValue exp(ASTNode value)
          throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

factorial

ASTNodeValue factorial(ASTNode value)
                throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

floor

ASTNodeValue floor(ASTNode value)
            throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

frac

ASTNodeValue frac(ASTNode numerator,
                  ASTNode denominator)
           throws SBMLException

Fraction of two ASTNodes

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<ASTNode> 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<ASTNode> args)
               throws SBMLException

Parameters:

functionDefinitionName -

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

Returns:

Throws:

SBMLException

geq

ASTNodeValue geq(ASTNode left,
                 ASTNode 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(ASTNode left,
                ASTNode right)
         throws SBMLException

Greater than.

Parameters:

left -

right -

Returns:

Throws:

SBMLException

lambda

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

The body of a FunctionDefinition.

Parameters:

values - Place holders for arguments.

Returns:

Throws:

SBMLException

leq

ASTNodeValue leq(ASTNode left,
                 ASTNode right)
          throws SBMLException

Less equal.

Parameters:

left -

right -

Returns:

Throws:

SBMLException

ln

ASTNodeValue ln(ASTNode value)
         throws SBMLException

Natural logarithm.

Parameters:

value -

Returns:

Throws:

SBMLException

log

ASTNodeValue log(ASTNode value)
          throws SBMLException

Logarithm of the given value to base 10.

Parameters:

value -

Returns:

Throws:

SBMLException

log

ASTNodeValue log(ASTNode base,
                 ASTNode value)
          throws SBMLException

Logarithm of the given value to the given base.

Parameters:

base -

value -

Returns:

Throws:

SBMLException

lt

ASTNodeValue lt(ASTNode left,
                ASTNode right)
         throws SBMLException

Less than.

Parameters:

left -

right -

Returns:

Throws:

SBMLException

minus

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

Subtraction.

Parameters:

values -

Returns:

Throws:

SBMLException

neq

ASTNodeValue neq(ASTNode left,
                 ASTNode right)
          throws SBMLException

Not equal.

Parameters:

left -

right -

Returns:

Throws:

SBMLException

not

ASTNodeValue not(ASTNode value)
          throws SBMLException

Parameters:

value - This value must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

or

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

Parameters:

values - These values must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

piecewise

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

Parameters:

values -

Returns:

Throws:

SBMLException

plus

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

Parameters:

values -

Returns:

Throws:

SBMLException

pow

ASTNodeValue pow(ASTNode base,
                 ASTNode exponent)
          throws SBMLException

Parameters:

base -

exponent -

Returns:

Throws:

SBMLException

root

ASTNodeValue root(ASTNode rootExponent,
                  ASTNode radiant)
           throws SBMLException

Parameters:

rootExponent -

radiant -

Returns:

Throws:

SBMLException

root

ASTNodeValue root(double rootExponent,
                  ASTNode radiant)
           throws SBMLException

Parameters:

rootExponent -

radiant -

Returns:

Throws:

SBMLException

sec

ASTNodeValue sec(ASTNode value)
          throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

sech

ASTNodeValue sech(ASTNode value)
           throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

selector

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

Parameters:

nodes -

Returns:

Throws:

SBMLException

sin

ASTNodeValue sin(ASTNode value)
          throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

sinh

ASTNodeValue sinh(ASTNode value)
           throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

sqrt

ASTNodeValue sqrt(ASTNode 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(ASTNode value)
          throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

tanh

ASTNodeValue tanh(ASTNode value)
           throws SBMLException

Parameters:

value -

Returns:

Throws:

SBMLException

times

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

Product of all given ASTNodes.

Parameters:

values - These values must be interpretable to Number.

Returns:

Throws:

SBMLException

uMinus

ASTNodeValue uMinus(ASTNode value)
             throws SBMLException

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

Parameters:

value -

Returns:

Throws:

SBMLException

unknownValue

ASTNodeValue unknownValue()
                   throws SBMLException

Dealing with a malformed ASTNode.

Returns:

Throws:

SBMLException

vector

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

Dealing with a vector.

Parameters:

nodes -

Returns:

Throws:

SBMLException

xor

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

Exclusive or.

Parameters:

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

Returns:

Throws:

SBMLException

max

ASTNodeValue max(java.util.List<ASTNode> values)

Returns the maximum of the values.

Parameters:

values -

Returns:

the maximum of the values.

min

ASTNodeValue min(java.util.List<ASTNode> values)

Returns the minimum of the values.

Parameters:

values -

Returns:

the minimum of the values.

quotient

ASTNodeValue quotient(java.util.List<ASTNode> values)

Returns the quotient of the division of the values.

Parameters:

values -

Returns:

the quotient of the values.

Throws:

SBMLException - if there are not two and only two arguments and it is a problem for the ASTNodeCompiler.

rem

ASTNodeValue rem(java.util.List<ASTNode> values)

Returns the remainder of the division of the values.

Parameters:

values -

Returns:

the remainder of the division of the values.

Throws:

SBMLException - if there are not two and only two arguments and it is a problem for the ASTNodeCompiler.

implies

ASTNodeValue implies(java.util.List<ASTNode> values)

Returns the logical implies between two ASTNode.

Truth table:

 p   q  p→q
 
 T   T   T
 T   F   F
 F   T   T
 F   F   T

Parameters:

children -

Returns:

the logical implies between two ASTNode.

Throws:

SBMLException - if there are not two and only two arguments and it is a problem for the ASTNodeCompiler.

getRateOf

ASTNodeValue getRateOf(java.lang.String name)

Parameters:

name -

Returns: