org.simulator.sbml.astnode

Class ASTNodeInterpreter

java.lang.Object

org.simulator.sbml.astnode.ASTNodeInterpreter

public class ASTNodeInterpreter
extends Object

This class is an efficient ASTNodeInterpreter that takes the time of the calculation into account. It contains functions similar to the ASTNodeCompiler interface, which have the current time as additional argument.

Since:

1.0

Version:

$Rev: 205 $

Author:

Roland Keller

Field Summary

Fields

Modifier and Type	Field and Description
static Logger	logger A logger.

Constructor Summary

Constructors

Constructor and Description
ASTNodeInterpreter(SBMLValueHolder valueHolder)

Method Summary

Modifier and Type	Method and Description
double	abs(ASTNodeValue userObject, double time, double delay)
boolean	and(ASTNodeValue[] children, int size, double time)
double	arccos(ASTNodeValue userObject, double time, double delay)
double	arccosh(ASTNodeValue userObject, double time, double delay)
double	arccot(ASTNodeValue userObject, double time, double delay)
double	arccoth(ASTNodeValue userObject, double time, double delay)
double	arccsc(ASTNodeValue userObject, double time, double delay)
double	arccsch(ASTNodeValue userObject, double time, double delay)
double	arcsec(ASTNodeValue userObject, double time, double delay)
double	arcsech(ASTNodeValue userObject, double time, double delay)
double	arcsin(ASTNodeValue userObject, double time, double delay)
double	arcsinh(ASTNodeValue userObject, double time, double delay)
double	arctan(ASTNodeValue userObject, double time, double delay)
double	arctanh(ASTNodeValue userObject, double time, double delay)
double	ceiling(ASTNodeValue userObject, double time, double delay)
double	compile(double mantissa, int exponent, String units)
double	compile(double value, String units)
boolean	compileBoolean(org.sbml.jsbml.CallableSBase nsb, double time)
double	compileDouble(org.sbml.jsbml.CallableSBase nsb, double time, double delay)
double	compileDouble(String name, double time, double delay)
String	compileString(org.sbml.jsbml.ASTNode child)
String	compileString(ASTNodeValue child)
double	cos(ASTNodeValue userObject, double time, double delay)
double	cosh(ASTNodeValue userObject, double time, double delay)
double	cot(ASTNodeValue userObject, double time, double delay)
double	coth(ASTNodeValue userObject, double time, double delay)
double	csc(ASTNodeValue userObject, double time, double delay)
double	csch(ASTNodeValue userObject, double time, double delay)
double	delay(ASTNodeValue x, ASTNodeValue delay, String timeUnits, double time)
boolean	eq(ASTNodeValue[] children, double time)
double	exp(ASTNodeValue userObject, double time, double delay)
double	factorial(ASTNodeValue userObject, double time, double delay)
double	floor(ASTNodeValue userObject, double time, double delay)
double	frac(ASTNodeValue left, ASTNodeValue right, double time, double delay)
double	frac(int numerator, int denominator)
boolean	functionBoolean(ASTNodeValue rightChild, List<String> variables, ASTNodeValue[] children, double[] values, double time)
boolean	functionBoolean(String name, List<ASTNodeValue> children)
double	functionDouble(ASTNodeValue rightChild, List<String> variables, ASTNodeValue[] children, int nArguments, double[] values, double time, double delay)
double	functionDouble(String functionDefinitionName, List<ASTNodeValue> args, double time)
boolean	geq(ASTNodeValue[] children, double time)
boolean	gt(ASTNodeValue[] children, double time)
double	implies(ASTNodeValue antecedent, ASTNodeValue consequent, double time, double delay)
boolean	lambdaBoolean(ASTNodeValue[] children, double time)
double	lambdaDouble(ASTNodeValue[] children, double time)
boolean	leq(ASTNodeValue[] children, double time)
double	ln(ASTNodeValue userObject, double time, double delay)
double	log(ASTNodeValue left, ASTNodeValue right, double time, double delay)
double	log(ASTNodeValue userObject, double time, double delay)
boolean	lt(ASTNodeValue[] children, double time)
double	maximum(ASTNodeValue[] children, double time, double delay)
double	minimum(ASTNodeValue[] children, double time, double delay)
double	minus(ASTNodeValue[] children, int size, double time, double delay)
boolean	neq(ASTNodeValue[] children, double time)
boolean	not(ASTNodeValue node, double time)
boolean	or(ASTNodeValue[] children, double time)
double	piecewise(ASTNodeValue[] children, double time, double delay)
double	plus(ASTNodeValue[] children, int size, double time, double delay)
double	pow(ASTNodeValue left, ASTNodeValue right, double time, double delay)
double	quotient(ASTNodeValue dividend, ASTNodeValue divisor, double time, double delay)
double	rateOf(EquationSystem eqnSystem, org.sbml.jsbml.CallableSBase sBase, double time, double delay)
double	remainder(ASTNodeValue dividend, ASTNodeValue divisor, double time, double delay)
double	root(ASTNodeValue rootExponent, ASTNodeValue radiant, double time, double delay)
double	root(double rootExponent, ASTNodeValue userObject, double time, double delay)
double	sec(ASTNodeValue userObject, double time, double delay)
double	sech(ASTNodeValue userObject, double time, double delay)
double	sin(ASTNodeValue userObject, double time, double delay)
double	sinh(ASTNodeValue userObject, double time, double delay)
double	sqrt(ASTNodeValue userObject, double time, double delay)
double	symbolTime()
double	tan(ASTNodeValue userObject, double time, double delay)
double	tanh(ASTNodeValue userObject, double time, double delay)
double	times(ASTNodeValue[] children, int size, double time, double delay)
String	toString(org.sbml.jsbml.ASTNode value)
double	uMinus(ASTNodeValue userObject, double time, double delay)
boolean	xor(ASTNodeValue[] children, double time)

Methods inherited from class java.lang.Object

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

Field Detail

logger

public static final Logger logger

A logger.

Constructor Detail

ASTNodeInterpreter

public ASTNodeInterpreter(SBMLValueHolder valueHolder)

Parameters:

valueHolder -

Method Detail

toString

public final String toString(org.sbml.jsbml.ASTNode value)

Parameters:

value -

Returns:

stringValue the interpreted String value of the node

compileDouble

public double compileDouble(String name,
                            double time,
                            double delay)

Parameters:

name -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

compileDouble

public double compileDouble(org.sbml.jsbml.CallableSBase nsb,
                            double time,
                            double delay)

Parameters:

nsb -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

compileBoolean

public boolean compileBoolean(org.sbml.jsbml.CallableSBase nsb,
                              double time)

Parameters:

nsb -

time -

Returns:

booleanValue the interpreted boolean value of the node

functionDouble

public double functionDouble(ASTNodeValue rightChild,
                             List<String> variables,
                             ASTNodeValue[] children,
                             int nArguments,
                             double[] values,
                             double time,
                             double delay)

Parameters:

rightChild -

variables -

children -

nArguments -

values -

time -

Returns:

doubleValue the interpreted double value of the node

compileString

public String compileString(ASTNodeValue child)

Parameters:

child -

Returns:

stringValue the interpreted String value of the node

compileString

public String compileString(org.sbml.jsbml.ASTNode child)

Parameters:

child -

Returns:

stringValue the interpreted String value of the node

lambdaDouble

public double lambdaDouble(ASTNodeValue[] children,
                           double time)

Parameters:

children -

time -

Returns:

doubleValue the interpreted double value of the node

lambdaBoolean

public boolean lambdaBoolean(ASTNodeValue[] children,
                             double time)

Parameters:

children -

time -

Returns:

booleanValue the interpreted boolean value of the node

piecewise

public double piecewise(ASTNodeValue[] children,
                        double time,
                        double delay)

Parameters:

children -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

log

public double log(ASTNodeValue userObject,
                  double time,
                  double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

log

public double log(ASTNodeValue left,
                  ASTNodeValue right,
                  double time,
                  double delay)

Parameters:

left -

right -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

functionDouble

public double functionDouble(String functionDefinitionName,
                             List<ASTNodeValue> args,
                             double time)

Parameters:

functionDefinitionName -

args -

time -

Returns:

doubleValue the interpreted double value of the nodedoubleValue the interpreted double value of the node

quotient

public double quotient(ASTNodeValue dividend,
                       ASTNodeValue divisor,
                       double time,
                       double delay)

Parameters:

dividend -

divisor -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

remainder

public double remainder(ASTNodeValue dividend,
                        ASTNodeValue divisor,
                        double time,
                        double delay)

Parameters:

dividend -

divisor -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

maximum

public double maximum(ASTNodeValue[] children,
                      double time,
                      double delay)

Parameters:

children -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

minimum

public double minimum(ASTNodeValue[] children,
                      double time,
                      double delay)

Parameters:

children -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

implies

public double implies(ASTNodeValue antecedent,
                      ASTNodeValue consequent,
                      double time,
                      double delay)

Parameters:

antecedent -

consequent -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

tanh

public double tanh(ASTNodeValue userObject,
                   double time,
                   double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

tan

public double tan(ASTNodeValue userObject,
                  double time,
                  double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

sinh

public double sinh(ASTNodeValue userObject,
                   double time,
                   double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

sin

public double sin(ASTNodeValue userObject,
                  double time,
                  double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

sech

public double sech(ASTNodeValue userObject,
                   double time,
                   double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

sec

public double sec(ASTNodeValue userObject,
                  double time,
                  double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

root

public double root(ASTNodeValue rootExponent,
                   ASTNodeValue radiant,
                   double time,
                   double delay)

Parameters:

rootExponent -

radiant -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

root

public double root(double rootExponent,
                   ASTNodeValue userObject,
                   double time,
                   double delay)

Parameters:

rootExponent -

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

ln

public double ln(ASTNodeValue userObject,
                 double time,
                 double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

floor

public double floor(ASTNodeValue userObject,
                    double time,
                    double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

factorial

public double factorial(ASTNodeValue userObject,
                        double time,
                        double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

exp

public double exp(ASTNodeValue userObject,
                  double time,
                  double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

csch

public double csch(ASTNodeValue userObject,
                   double time,
                   double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

csc

public double csc(ASTNodeValue userObject,
                  double time,
                  double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

coth

public double coth(ASTNodeValue userObject,
                   double time,
                   double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

cot

public double cot(ASTNodeValue userObject,
                  double time,
                  double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

cosh

public double cosh(ASTNodeValue userObject,
                   double time,
                   double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

cos

public double cos(ASTNodeValue userObject,
                  double time,
                  double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

ceiling

public double ceiling(ASTNodeValue userObject,
                      double time,
                      double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

arctanh

public double arctanh(ASTNodeValue userObject,
                      double time,
                      double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

functionBoolean

public boolean functionBoolean(String name,
                               List<ASTNodeValue> children)

Parameters:

name -

children -

Returns:

booleanValue the interpreted boolean value of the node

functionBoolean

public boolean functionBoolean(ASTNodeValue rightChild,
                               List<String> variables,
                               ASTNodeValue[] children,
                               double[] values,
                               double time)

Parameters:

rightChild -

variables -

children -

values -

time -

Returns:

booleanValue the interpreted boolean value of the node

lt

public boolean lt(ASTNodeValue[] children,
                  double time)

Parameters:

children -

time -

Returns:

booleanValue the interpreted boolean value of the node

leq

public boolean leq(ASTNodeValue[] children,
                   double time)

Parameters:

children -

time -

Returns:

booleanValue the interpreted boolean value of the node

neq

public boolean neq(ASTNodeValue[] children,
                   double time)

Parameters:

children -

time -

Returns:

booleanValue the interpreted boolean value of the node

gt

public boolean gt(ASTNodeValue[] children,
                  double time)

Parameters:

children -

time -

Returns:

booleanValue the interpreted boolean value of the node

geq

public boolean geq(ASTNodeValue[] children,
                   double time)

Parameters:

children -

time -

Returns:

booleanValue the interpreted boolean value of the node

eq

public boolean eq(ASTNodeValue[] children,
                  double time)

Parameters:

children -

time -

Returns:

booleanValue the interpreted boolean value of the node

not

public boolean not(ASTNodeValue node,
                   double time)

Parameters:

node -

time -

Returns:

booleanValue the interpreted boolean value of the node

or

public boolean or(ASTNodeValue[] children,
                  double time)

Parameters:

children -

time -

Returns:

booleanValue the interpreted boolean value of the node

xor

public boolean xor(ASTNodeValue[] children,
                   double time)

Parameters:

children -

time -

Returns:

booleanValue the interpreted boolean value of the node

and

public boolean and(ASTNodeValue[] children,
                   int size,
                   double time)

Parameters:

children -

time -

Returns:

booleanValue the interpreted boolean value of the node

arctan

public double arctan(ASTNodeValue userObject,
                     double time,
                     double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

arcsinh

public double arcsinh(ASTNodeValue userObject,
                      double time,
                      double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

arcsin

public double arcsin(ASTNodeValue userObject,
                     double time,
                     double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

arcsech

public double arcsech(ASTNodeValue userObject,
                      double time,
                      double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

arcsec

public double arcsec(ASTNodeValue userObject,
                     double time,
                     double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

arccsch

public double arccsch(ASTNodeValue userObject,
                      double time,
                      double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

arccsc

public double arccsc(ASTNodeValue userObject,
                     double time,
                     double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

arccoth

public double arccoth(ASTNodeValue userObject,
                      double time,
                      double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

arccot

public double arccot(ASTNodeValue userObject,
                     double time,
                     double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

arccosh

public double arccosh(ASTNodeValue userObject,
                      double time,
                      double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

arccos

public double arccos(ASTNodeValue userObject,
                     double time,
                     double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

abs

public double abs(ASTNodeValue userObject,
                  double time,
                  double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

compile

public double compile(double mantissa,
                      int exponent,
                      String units)

Parameters:

mantissa -

exponent -

units -

Returns:

doubleValue the interpreted double value of the node

delay

public final double delay(ASTNodeValue x,
                          ASTNodeValue delay,
                          String timeUnits,
                          double time)

Parameters:

x -

delay -

timeUnits -

time -

Returns:

doubleValue the interpreted double value of the node

symbolTime

public double symbolTime()

Returns:

doubleValue the interpreted double value of the node

frac

public double frac(int numerator,
                   int denominator)

Parameters:

numerator -

denominator -

Returns:

doubleValue the interpreted double value of the node

frac

public double frac(ASTNodeValue left,
                   ASTNodeValue right,
                   double time,
                   double delay)

Parameters:

left -

right -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

times

public double times(ASTNodeValue[] children,
                    int size,
                    double time,
                    double delay)

Parameters:

children -

size -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

minus

public double minus(ASTNodeValue[] children,
                    int size,
                    double time,
                    double delay)

Parameters:

children -

size -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

plus

public double plus(ASTNodeValue[] children,
                   int size,
                   double time,
                   double delay)

Parameters:

children -

size -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

pow

public double pow(ASTNodeValue left,
                  ASTNodeValue right,
                  double time,
                  double delay)

Parameters:

left -

right -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

compile

public double compile(double value,
                      String units)

Parameters:

value -

units -

Returns:

doubleValue the interpreted double value of the node

sqrt

public double sqrt(ASTNodeValue userObject,
                   double time,
                   double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

uMinus

public double uMinus(ASTNodeValue userObject,
                     double time,
                     double delay)

Parameters:

userObject -

time -

delay -

Returns:

doubleValue the interpreted double value of the node

rateOf

public double rateOf(EquationSystem eqnSystem,
                     org.sbml.jsbml.CallableSBase sBase,
                     double time,
                     double delay)

Parameters:

eqnSystem -

sBase -

time -

Returns:

doubleValue the interpreted double value of the node