org.simulator.sbml.astnode
Class StoichiometryObject

java.lang.Object
  org.simulator.sbml.astnode.StoichiometryObject

public class StoichiometryObject
extends java.lang.Object

Computes for a species reference with a stoichiometry occuring in some reaction the stoichiometry and the change of the corresponding species that is caused by the reaction.

Version:

$Rev: 149 $

Author:

Roland Keller

Field Summary

protected ValueHolder

valueHolder The value holder that stores the current simulation results.

Constructor Summary

StoichiometryObject(org.sbml.jsbml.SpeciesReference sr, int speciesIndex, int speciesRefIndex, int compartmentIndex, java.util.Map<java.lang.String,java.lang.Double> stoichiometricCoefHash, ValueHolder valueHolder, double[] Y, EfficientASTNodeInterpreter nodeInterpreter, int reactionIndex, java.util.Set<java.lang.String> inConcentrationSet, boolean isReactant)

Method Summary

void	computeChange(double currentTime, double[] changeRate, double[] v) Computes the change resulting for the corresponding species in this reaction at the current time and stores it at the correct position in the changeRate array.
void	refresh() Refreshes the stoichiometry.

Methods inherited from class java.lang.Object

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

Field Detail

valueHolder

protected ValueHolder valueHolder

The value holder that stores the current simulation results.

Constructor Detail

StoichiometryObject

public StoichiometryObject(org.sbml.jsbml.SpeciesReference sr,
                           int speciesIndex,
                           int speciesRefIndex,
                           int compartmentIndex,
                           java.util.Map<java.lang.String,java.lang.Double> stoichiometricCoefHash,
                           ValueHolder valueHolder,
                           double[] Y,
                           EfficientASTNodeInterpreter nodeInterpreter,
                           int reactionIndex,
                           java.util.Set<java.lang.String> inConcentrationSet,
                           boolean isReactant)

Parameters:

sr -

speciesIndex -

speciesRefIndex -

compartmentIndex -

stoichiometricCoefHash -

valueHolder -

Y -

nodeInterpreter -

reactionIndex -

inConcentrationSet -

isReactant -

Method Detail

computeChange

public void computeChange(double currentTime,
                          double[] changeRate,
                          double[] v)

Computes the change resulting for the corresponding species in this reaction at the current time and stores it at the correct position in the changeRate array.

Parameters:

currentTime -

changeRate -

v -

refresh

public void refresh()

Refreshes the stoichiometry.