org.systemsbiology.chem
Class SimulatorStochasticGillespie

java.lang.Object
  extended byorg.systemsbiology.chem.Simulator
      extended byorg.systemsbiology.chem.SimulatorStochasticBase
          extended byorg.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