broadwick.stochastic.algorithms

Class AbstractTauLeapingBase

java.lang.Object

broadwick.stochastic.StochasticSimulator

broadwick.stochastic.algorithms.AbstractTauLeapingBase

Direct Known Subclasses:

TauLeaping, TauLeapingFixedStep

public abstract class AbstractTauLeapingBase
extends StochasticSimulator

Abstract base class for tau leaping classes.

Field Summary

Fields

Modifier and Type	Field and Description
protected static RNG	GENERATOR

Fields inherited from class broadwick.stochastic.StochasticSimulator

reverseTime

Constructor Summary

Constructors

Constructor and Description
AbstractTauLeapingBase(AmountManager amountManager, TransitionKernel transitionKernel) Create the tau-leaping object.

Method Summary

Modifier and Type	Method and Description
protected boolean	isThetaEventInCurrentStep(double tau) Determine of there is a theta event in the current time step, taking into account possible reverse time jumps.
protected void	updateStates(double tau) Update all the reactions/transitions that have occurred in the tau step.

Methods inherited from class broadwick.stochastic.StochasticSimulator

addObserver, doEvent, doEvent, doThetaEvent, getDefaultObserver, getName, getNextThetaEventTime, init, performStep, registerNewTheta, reinitialize, run, run, setRngSeed

Methods inherited from class java.lang.Object

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

Field Detail

GENERATOR

protected static final RNG GENERATOR

Constructor Detail

AbstractTauLeapingBase

public AbstractTauLeapingBase(AmountManager amountManager,
                              TransitionKernel transitionKernel)

Create the tau-leaping object.

Parameters:

amountManager - the amount manager used in the simulator.

transitionKernel - the transition kernel to be used with the stochastic solver.

Method Detail

updateStates

protected final void updateStates(double tau)

Update all the reactions/transitions that have occurred in the tau step.

Parameters:

tau - the step size.

isThetaEventInCurrentStep

protected final boolean isThetaEventInCurrentStep(double tau)

Determine of there is a theta event in the current time step, taking into account possible reverse time jumps.

Parameters:

tau - the time interval (will be negative for reverse time).

Returns:

true if a theta event is found.