org.systemsbiology.chem
Class SimulatorStochasticGillespie

java.lang.Object
  org.systemsbiology.chem.Simulator
      org.systemsbiology.chem.SimulatorStochasticBase
          org.systemsbiology.chem.SimulatorStochasticGillespie

All Implemented Interfaces:

IAliasableClass, ISimulator

public final class SimulatorStochasticGillespie

extends SimulatorStochasticBase

implements IAliasableClass, ISimulator

Simulates the dynamics of a set of coupled chemical reactions described by Reaction objects using the Gillespie stochastic algorithm, "direct method".

Author:

Stephen Ramsey

Field Summary

static String

CLASS_ALIAS

Fields inherited from class org.systemsbiology.chem.SimulatorStochasticBase

DEFAULT_ENSEMBLE_SIZE, DEFAULT_FLAG_GET_FINAL_SYMBOL_FLUCTUATIONS, DEFAULT_NUM_HISTORY_BINS, mDynamicSymbolDelayedReactionAssociations, mPoissonEventGenerator, mRandomNumberGenerator

Fields inherited from class org.systemsbiology.chem.Simulator

DEFAULT_MIN_NUM_MILLISECONDS_FOR_UPDATE, mDelayedReactionSolvers, mDynamicSymbolAdjustmentVectors, mDynamicSymbolNames, mDynamicSymbols, mDynamicSymbolValues, mInitialDynamicSymbolValues, mInitialized, mIsStochasticSimulator, mMinNumMillisecondsForUpdate, mModelName, mNonDynamicSymbolExpressionValues, mNonDynamicSymbolValues, mReactionProbabilities, mReactionRates, mReactions, mReactionsDelayedReactionAssociations, mReactionsLocalParamSymbolsMaps, mReactionsProductsDynamic, mReactionsProductsSpecies, mReactionsProductsStoichiometries, mReactionsReactantsDynamic, mReactionsReactantsSpecies, mReactionsReactantsStoichiometries, mReactionSymbols, mSimulationController, mSimulationProgressReporter, mSymbolEvaluator, mSymbolMap, mUseExpressionValueCaching, NULL_REACTION

Fields inherited from interface org.systemsbiology.chem.ISimulator

MIN_NUM_RESULTS_TIME_POINTS

Constructor Summary

SimulatorStochasticGillespie()

Method Summary

String	getAlias()
void	initialize(Model pModel)
protected double	iterate(MutableInteger pLastReactionIndex)
protected void	modifyDefaultSimulatorParameters(SimulatorParameters pSimulatorParameters)
protected void	prepareForStochasticSimulation(double pStartTime, SimulatorParameters pSimulatorParameters)

Methods inherited from class org.systemsbiology.chem.SimulatorStochasticBase

allowsInterrupt, checkDynamicalSymbolsValues, checkSimulationParametersImpl, chooseDeltaTimeToNextReaction, chooseIndexOfNextReaction, getDefaultSimulatorParameters, getNextDelayedReactionIndex, getPoissonEvent, getRandomNumberGenerator, getRandomNumberUniformInterval, initializePoissonEventGenerator, initializeRandomNumberGenerator, initializeSimulatorStochastic, isStochasticSimulator, setRandomNumberGenerator, simulate, updateSymbolValuesForReaction

Methods inherited from class org.systemsbiology.chem.Simulator

addRequestedSymbolValues, canComputeFluctuations, checkSimulationParameters, checkSimulationParametersForDeterministicSimulator, clearExpressionValueCaches, clearSimulatorState, computeDerivative, computeRatePartialDerivativeExpression, computeReactionProbabilities, createRequestedSymbolArray, createSimulationResults, createTimesArray, getDelayedReactionEstimatedAverageFutureRate, getMinDelayedReactionDelay, getReactionRateExpressions, hasDelayedReactionSolvers, initializeDynamicSymbolAdjustmentVectors, initializeSimulator, isInitialized, prepareForSimulation, resizeDelayedReactionSolvers, setController, setInitialized, setMinNumMillisecondsForUpdate, setProgressReporter, setStatusUpdateIntervalSeconds

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.systemsbiology.chem.ISimulator

allowsInterrupt, canComputeFluctuations, checkSimulationParameters, getDefaultSimulatorParameters, isInitialized, setController, setProgressReporter, setStatusUpdateIntervalSeconds, simulate

Field Detail

CLASS_ALIAS

public static final String CLASS_ALIAS

See Also:

Constant Field Values

Constructor Detail

SimulatorStochasticGillespie

public SimulatorStochasticGillespie()

Method Detail

prepareForStochasticSimulation

protected void prepareForStochasticSimulation(double pStartTime,
                                              SimulatorParameters pSimulatorParameters)

Specified by:

prepareForStochasticSimulation in class SimulatorStochasticBase

iterate

protected double iterate(MutableInteger pLastReactionIndex)
                  throws DataNotFoundException,
                         IllegalStateException

Specified by:

iterate in class SimulatorStochasticBase

Throws:

DataNotFoundException

IllegalStateException

initialize

public void initialize(Model pModel)
                throws DataNotFoundException,
                       InvalidInputException

Specified by:

initialize in interface ISimulator

Throws:

DataNotFoundException

InvalidInputException

modifyDefaultSimulatorParameters

protected void modifyDefaultSimulatorParameters(SimulatorParameters pSimulatorParameters)

Specified by:

modifyDefaultSimulatorParameters in class SimulatorStochasticBase

getAlias

public String getAlias()

Specified by:

getAlias in interface ISimulator

Specified by:

getAlias in class Simulator