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org.simulator.sbml.astnode
Class ASTNodeInterpreterWithTime

java.lang.Object
  extended by org.simulator.sbml.astnode.ASTNodeInterpreterWithTime

public class ASTNodeInterpreterWithTime
extends java.lang.Object

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

Since:
1.0
Version:
$Rev: 22 $
Author:
Roland Keller

Field Summary
static java.util.logging.Logger logger
          A logger.
 
Constructor Summary
ASTNodeInterpreterWithTime(ValueHolder valueHolder)
           
 
Method Summary
 double abs(ASTNodeObject userObject, double time)
           
 boolean and(java.util.List<ASTNodeObject> nodes, int size, double time)
           
 double arccos(ASTNodeObject userObject, double time)
           
 double arccosh(ASTNodeObject userObject, double time)
           
 double arccot(ASTNodeObject userObject, double time)
           
 double arccoth(ASTNodeObject userObject, double time)
           
 double arccsc(ASTNodeObject userObject, double time)
           
 double arccsch(ASTNodeObject userObject, double time)
           
 double arcsec(ASTNodeObject userObject, double time)
           
 double arcsech(ASTNodeObject userObject, double time)
           
 double arcsin(ASTNodeObject userObject, double time)
           
 double arcsinh(ASTNodeObject userObject, double time)
           
 double arctan(ASTNodeObject userObject, double time)
           
 double arctanh(ASTNodeObject userObject, double time)
           
 double ceiling(ASTNodeObject userObject, double time)
           
 double compile(double mantissa, int exponent, java.lang.String units)
           
 double compile(double value, java.lang.String units)
           
 boolean compileBoolean(org.sbml.jsbml.CallableSBase nsb, double time)
           
 double compileDouble(org.sbml.jsbml.CallableSBase nsb, double time)
           
 double compileDouble(java.lang.String name, double time)
           
 java.lang.String compileString(org.sbml.jsbml.ASTNode child)
           
 java.lang.String compileString(ASTNodeObject child)
           
 double cos(ASTNodeObject userObject, double time)
           
 double cosh(ASTNodeObject userObject, double time)
           
 double cot(ASTNodeObject userObject, double time)
           
 double coth(ASTNodeObject userObject, double time)
           
 double csc(ASTNodeObject userObject, double time)
           
 double csch(ASTNodeObject userObject, double time)
           
 double delay(java.lang.String delayName, ASTNodeObject x, ASTNodeObject delay, java.lang.String timeUnits, double time)
           
 boolean eq(ASTNodeObject left, ASTNodeObject right, double time)
           
 double exp(ASTNodeObject userObject, double time)
           
 double factorial(ASTNodeObject userObject, double time)
           
 double floor(ASTNodeObject userObject, double time)
           
 double frac(ASTNodeObject left, ASTNodeObject right, double time)
           
 double frac(int numerator, int denominator)
           
 boolean functionBoolean(ASTNodeObject rightChild, java.util.List<java.lang.String> variables, java.util.List<ASTNodeObject> arguments, double[] values, double time)
           
 boolean functionBoolean(java.lang.String name, java.util.List<ASTNodeObject> children)
           
 double functionDouble(ASTNodeObject rightChild, java.util.List<java.lang.String> variables, java.util.List<ASTNodeObject> arguments, int nArguments, double[] values, double time)
           
 double functionDouble(java.lang.String functionDefinitionName, java.util.List<ASTNodeObject> args, double time)
           
 boolean geq(ASTNodeObject left, ASTNodeObject right, double time)
           
 boolean gt(ASTNodeObject left, ASTNodeObject right, double time)
           
 boolean lambdaBoolean(java.util.List<ASTNodeObject> nodes, double time)
           
 double lambdaDouble(java.util.List<ASTNodeObject> nodes, double time)
           
 boolean leq(ASTNodeObject left, ASTNodeObject right, double time)
           
 double ln(ASTNodeObject userObject, double time)
           
 double log(ASTNodeObject left, ASTNodeObject right, double time)
           
 double log(ASTNodeObject userObject, double time)
           
 boolean lt(ASTNodeObject left, ASTNodeObject right, double time)
           
 double minus(java.util.List<ASTNodeObject> nodes, int size, double time)
           
 boolean neq(ASTNodeObject left, ASTNodeObject right, double time)
           
 boolean not(ASTNodeObject node, double time)
           
 boolean or(java.util.List<ASTNodeObject> nodes, double time)
           
 double piecewise(java.util.List<ASTNodeObject> nodes, double time)
           
 double plus(java.util.List<ASTNodeObject> nodes, int size, double time)
           
 double pow(ASTNodeObject left, ASTNodeObject right, double time)
           
 double root(ASTNodeObject rootExponent, ASTNodeObject radiant, double time)
           
 double root(double rootExponent, ASTNodeObject userObject, double time)
           
 double sec(ASTNodeObject userObject, double time)
           
 double sech(ASTNodeObject userObject, double time)
           
 double sin(ASTNodeObject userObject, double time)
           
 double sinh(ASTNodeObject userObject, double time)
           
 double sqrt(ASTNodeObject userObject, double time)
           
 double symbolTime(java.lang.String name)
           
 double tan(ASTNodeObject userObject, double time)
           
 double tanh(ASTNodeObject userObject, double time)
           
 double times(java.util.List<ASTNodeObject> nodes, int size, double time)
           
 java.lang.String toString(org.sbml.jsbml.ASTNode value)
           
 double uMinus(ASTNodeObject userObject, double time)
           
 boolean xor(java.util.List<ASTNodeObject> nodes, double time)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

logger

public static final java.util.logging.Logger logger
A logger.

Constructor Detail

ASTNodeInterpreterWithTime

public ASTNodeInterpreterWithTime(ValueHolder valueHolder)
Parameters:
valueHolder -
Method Detail

toString

public final java.lang.String toString(org.sbml.jsbml.ASTNode value)
Parameters:
value -
Returns:

compileDouble

public double compileDouble(java.lang.String name,
                            double time)
Parameters:
name -
time -
Returns:

compileDouble

public double compileDouble(org.sbml.jsbml.CallableSBase nsb,
                            double time)
                     throws org.sbml.jsbml.SBMLException
Parameters:
nsb -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

compileBoolean

public boolean compileBoolean(org.sbml.jsbml.CallableSBase nsb,
                              double time)
                       throws org.sbml.jsbml.SBMLException
Parameters:
nsb -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

functionDouble

public double functionDouble(ASTNodeObject rightChild,
                             java.util.List<java.lang.String> variables,
                             java.util.List<ASTNodeObject> arguments,
                             int nArguments,
                             double[] values,
                             double time)
                      throws org.sbml.jsbml.SBMLException
Parameters:
rightChild -
variables -
arguments -
nArguments -
values -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

compileString

public java.lang.String compileString(ASTNodeObject child)
Parameters:
child -
Returns:

compileString

public java.lang.String compileString(org.sbml.jsbml.ASTNode child)
Parameters:
child -
Returns:

lambdaDouble

public double lambdaDouble(java.util.List<ASTNodeObject> nodes,
                           double time)
                    throws org.sbml.jsbml.SBMLException
Parameters:
nodes -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

lambdaBoolean

public boolean lambdaBoolean(java.util.List<ASTNodeObject> nodes,
                             double time)
                      throws org.sbml.jsbml.SBMLException
Parameters:
nodes -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

piecewise

public double piecewise(java.util.List<ASTNodeObject> nodes,
                        double time)
                 throws org.sbml.jsbml.SBMLException
Parameters:
nodes -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

log

public double log(ASTNodeObject userObject,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

log

public double log(ASTNodeObject left,
                  ASTNodeObject right,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
left -
right -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

functionDouble

public double functionDouble(java.lang.String functionDefinitionName,
                             java.util.List<ASTNodeObject> args,
                             double time)
                      throws org.sbml.jsbml.SBMLException
Parameters:
functionDefinitionName -
args -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

tanh

public double tanh(ASTNodeObject userObject,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

tan

public double tan(ASTNodeObject userObject,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

sinh

public double sinh(ASTNodeObject userObject,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

sin

public double sin(ASTNodeObject userObject,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

sech

public double sech(ASTNodeObject userObject,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

sec

public double sec(ASTNodeObject userObject,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

root

public double root(ASTNodeObject rootExponent,
                   ASTNodeObject radiant,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
rootExponent -
radiant -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

root

public double root(double rootExponent,
                   ASTNodeObject userObject,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
rootExponent -
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

ln

public double ln(ASTNodeObject userObject,
                 double time)
          throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

floor

public double floor(ASTNodeObject userObject,
                    double time)
             throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

factorial

public double factorial(ASTNodeObject userObject,
                        double time)
                 throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

exp

public double exp(ASTNodeObject userObject,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

csch

public double csch(ASTNodeObject userObject,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

csc

public double csc(ASTNodeObject userObject,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

coth

public double coth(ASTNodeObject userObject,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

cot

public double cot(ASTNodeObject userObject,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

cosh

public double cosh(ASTNodeObject userObject,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

cos

public double cos(ASTNodeObject userObject,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

ceiling

public double ceiling(ASTNodeObject userObject,
                      double time)
               throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

arctanh

public double arctanh(ASTNodeObject userObject,
                      double time)
               throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

functionBoolean

public boolean functionBoolean(java.lang.String name,
                               java.util.List<ASTNodeObject> children)
Parameters:
name -
children -
Returns:

functionBoolean

public boolean functionBoolean(ASTNodeObject rightChild,
                               java.util.List<java.lang.String> variables,
                               java.util.List<ASTNodeObject> arguments,
                               double[] values,
                               double time)
                        throws org.sbml.jsbml.SBMLException
Parameters:
rightChild -
variables -
arguments -
values -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

lt

public boolean lt(ASTNodeObject left,
                  ASTNodeObject right,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
left -
right -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

leq

public boolean leq(ASTNodeObject left,
                   ASTNodeObject right,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
left -
right -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

neq

public boolean neq(ASTNodeObject left,
                   ASTNodeObject right,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
left -
right -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

gt

public boolean gt(ASTNodeObject left,
                  ASTNodeObject right,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
left -
right -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

geq

public boolean geq(ASTNodeObject left,
                   ASTNodeObject right,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
left -
right -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

eq

public boolean eq(ASTNodeObject left,
                  ASTNodeObject right,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
left -
right -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

not

public boolean not(ASTNodeObject node,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
node -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

or

public boolean or(java.util.List<ASTNodeObject> nodes,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
nodes -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

xor

public boolean xor(java.util.List<ASTNodeObject> nodes,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
nodes -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

and

public boolean and(java.util.List<ASTNodeObject> nodes,
                   int size,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
nodes -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

arctan

public double arctan(ASTNodeObject userObject,
                     double time)
              throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

arcsinh

public double arcsinh(ASTNodeObject userObject,
                      double time)
               throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

arcsin

public double arcsin(ASTNodeObject userObject,
                     double time)
              throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

arcsech

public double arcsech(ASTNodeObject userObject,
                      double time)
               throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

arcsec

public double arcsec(ASTNodeObject userObject,
                     double time)
              throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

arccsch

public double arccsch(ASTNodeObject userObject,
                      double time)
               throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

arccsc

public double arccsc(ASTNodeObject userObject,
                     double time)
              throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

arccoth

public double arccoth(ASTNodeObject userObject,
                      double time)
               throws org.sbml.jsbml.SBMLException
Parameters:
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

arccot

public double arccot(ASTNodeObject userObject,
                     double time)
              throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

arccosh

public double arccosh(ASTNodeObject userObject,
                      double time)
               throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

arccos

public double arccos(ASTNodeObject userObject,
                     double time)
              throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

abs

public double abs(ASTNodeObject userObject,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

compile

public double compile(double mantissa,
                      int exponent,
                      java.lang.String units)
Parameters:
mantissa -
exponent -
units -
Returns:

delay

public final double delay(java.lang.String delayName,
                          ASTNodeObject x,
                          ASTNodeObject delay,
                          java.lang.String timeUnits,
                          double time)
                   throws org.sbml.jsbml.SBMLException
Parameters:
delayName -
x -
delay -
timeUnits -
Returns:
Throws:
org.sbml.jsbml.SBMLException

symbolTime

public double symbolTime(java.lang.String name)
Parameters:
name -
Returns:

frac

public double frac(int numerator,
                   int denominator)
Parameters:
numerator -
denominator -
Returns:

frac

public double frac(ASTNodeObject left,
                   ASTNodeObject right,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
left -
right -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

times

public double times(java.util.List<ASTNodeObject> nodes,
                    int size,
                    double time)
             throws org.sbml.jsbml.SBMLException
Parameters:
nodes -
size -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

minus

public double minus(java.util.List<ASTNodeObject> nodes,
                    int size,
                    double time)
             throws org.sbml.jsbml.SBMLException
Parameters:
nodes -
size -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

plus

public double plus(java.util.List<ASTNodeObject> nodes,
                   int size,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
nodes -
size -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

pow

public double pow(ASTNodeObject left,
                  ASTNodeObject right,
                  double time)
           throws org.sbml.jsbml.SBMLException
Parameters:
left -
right -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

compile

public double compile(double value,
                      java.lang.String units)
Parameters:
value -
units -
Returns:

sqrt

public double sqrt(ASTNodeObject userObject,
                   double time)
            throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException

uMinus

public double uMinus(ASTNodeObject userObject,
                     double time)
              throws org.sbml.jsbml.SBMLException
Parameters:
userObject -
time -
Returns:
Throws:
org.sbml.jsbml.SBMLException
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