org.systemsbiology.chem.odetojava
Class SimulatorOdeToJavaRungeKuttaImplicit

java.lang.Object
  org.systemsbiology.chem.Simulator
      org.systemsbiology.chem.odetojava.SimulatorOdeToJavaBase
          org.systemsbiology.chem.odetojava.SimulatorOdeToJavaRungeKuttaImplicit

All Implemented Interfaces:

IAliasableClass, ISimulator, odeToJava.modules.ODE, odeToJava.modules.ODERecorder

public final class SimulatorOdeToJavaRungeKuttaImplicit

extends SimulatorOdeToJavaBase

implements IAliasableClass, ISimulator

Field Summary

static String

CLASS_ALIAS

Fields inherited from class org.systemsbiology.chem.odetojava.SimulatorOdeToJavaBase

DEFAULT_FLAG_GET_FINAL_SYMBOL_FLUCTUATIONS, DEFAULT_MAX_ALLOWED_ABSOLUTE_ERROR, DEFAULT_MAX_ALLOWED_RELATIVE_ERROR, DEFAULT_NUM_HISTORY_BINS

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

SimulatorOdeToJavaRungeKuttaImplicit()

Method Summary

boolean	allowsInterrupt()
String	getAlias()
protected void	runExternalSimulation(odeToJava.modules.Span pSimulationTimeSpan, double[] pInitialDynamicSymbolValues, double pInitialStepSize, double pMaxAllowedRelativeError, double pMaxAllowedAbsoluteError, String pTempOutputFileName)

Methods inherited from class org.systemsbiology.chem.odetojava.SimulatorOdeToJavaBase

checkSimulationParametersImpl, f, g, getDefaultSimulatorParameters, initialize, isStochasticSimulator, readSimulationOutput, record, simulate

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

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

Field Detail

CLASS_ALIAS

public static final String CLASS_ALIAS

See Also:

Constant Field Values

Constructor Detail

SimulatorOdeToJavaRungeKuttaImplicit

public SimulatorOdeToJavaRungeKuttaImplicit()

Method Detail

allowsInterrupt

public boolean allowsInterrupt()

Specified by:

allowsInterrupt in interface ISimulator

runExternalSimulation

protected void runExternalSimulation(odeToJava.modules.Span pSimulationTimeSpan,
                                     double[] pInitialDynamicSymbolValues,
                                     double pInitialStepSize,
                                     double pMaxAllowedRelativeError,
                                     double pMaxAllowedAbsoluteError,
                                     String pTempOutputFileName)

Specified by:

runExternalSimulation in class SimulatorOdeToJavaBase

getAlias

public String getAlias()

Specified by:

getAlias in interface ISimulator

Specified by:

getAlias in class Simulator