org.systemsbiology.chem.odetojava
Class SimulatorOdeToJavaBase

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

All Implemented Interfaces:

odeToJava.modules.ODE, odeToJava.modules.ODERecorder

Direct Known Subclasses:

SimulatorOdeToJavaRungeKuttaAdaptive, SimulatorOdeToJavaRungeKuttaImplicit

public abstract class SimulatorOdeToJavaBase

extends Simulator

implements odeToJava.modules.ODE, odeToJava.modules.ODERecorder

Field Summary

static boolean	DEFAULT_FLAG_GET_FINAL_SYMBOL_FLUCTUATIONS
static double	DEFAULT_MAX_ALLOWED_ABSOLUTE_ERROR
static double	DEFAULT_MAX_ALLOWED_RELATIVE_ERROR
protected static int	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

Constructor Summary

SimulatorOdeToJavaBase()

Method Summary

void	checkSimulationParametersImpl(SimulatorParameters pSimulatorParameters, int pNumResultsTimePoints)
double[]	f(double t, double[] x)
double[]	g(double t, double[] x)
SimulatorParameters	getDefaultSimulatorParameters()
void	initialize(Model pModel)
boolean	isStochasticSimulator()
protected void	readSimulationOutput(File pSimulationResultsFile, SymbolEvaluatorChem pSymbolEvaluator, double[] pDynamicSymbolValues, double pStartTime, double pEndTime, int pNumResultsTimePoints, Symbol[] pRequestedSymbols, double[] pRetResultsTimeValues, Object[] pRetResultsSymbolValues)
void	record(double t, double[] x)
protected abstract void	runExternalSimulation(odeToJava.modules.Span pSimulationTimeSpan, double[] pInitialDynamicSymbolValues, double pInitialStepSize, double pMaxAllowedRelativeError, double pMaxAllowedAbsoluteError, String pTempOutputFileName)
SimulationResults	simulate(double pStartTime, double pEndTime, SimulatorParameters pSimulatorParameters, int pNumResultsTimePoints, String[] pRequestedSymbolNames)

Methods inherited from class org.systemsbiology.chem.Simulator

addRequestedSymbolValues, canComputeFluctuations, checkSimulationParameters, checkSimulationParametersForDeterministicSimulator, clearExpressionValueCaches, clearSimulatorState, computeDerivative, computeRatePartialDerivativeExpression, computeReactionProbabilities, createRequestedSymbolArray, createSimulationResults, createTimesArray, getAlias, 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

Field Detail

DEFAULT_MAX_ALLOWED_RELATIVE_ERROR

public static final double DEFAULT_MAX_ALLOWED_RELATIVE_ERROR

See Also:

Constant Field Values

DEFAULT_MAX_ALLOWED_ABSOLUTE_ERROR

public static final double DEFAULT_MAX_ALLOWED_ABSOLUTE_ERROR

See Also:

Constant Field Values

DEFAULT_FLAG_GET_FINAL_SYMBOL_FLUCTUATIONS

public static final boolean DEFAULT_FLAG_GET_FINAL_SYMBOL_FLUCTUATIONS

See Also:

Constant Field Values

DEFAULT_NUM_HISTORY_BINS

protected static final int DEFAULT_NUM_HISTORY_BINS

See Also:

Constant Field Values

Constructor Detail

SimulatorOdeToJavaBase

public SimulatorOdeToJavaBase()

Method Detail

runExternalSimulation

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

simulate

public SimulationResults simulate(double pStartTime,
                                  double pEndTime,
                                  SimulatorParameters pSimulatorParameters,
                                  int pNumResultsTimePoints,
                                  String[] pRequestedSymbolNames)
                           throws DataNotFoundException,
                                  IllegalStateException,
                                  IllegalArgumentException,
                                  AccuracyException,
                                  SimulationFailedException

Throws:

DataNotFoundException

IllegalStateException

IllegalArgumentException

AccuracyException

SimulationFailedException

readSimulationOutput

protected void readSimulationOutput(File pSimulationResultsFile,
                                    SymbolEvaluatorChem pSymbolEvaluator,
                                    double[] pDynamicSymbolValues,
                                    double pStartTime,
                                    double pEndTime,
                                    int pNumResultsTimePoints,
                                    Symbol[] pRequestedSymbols,
                                    double[] pRetResultsTimeValues,
                                    Object[] pRetResultsSymbolValues)
                             throws InvalidInputException,
                                    DataNotFoundException,
                                    FileNotFoundException,
                                    IOException,
                                    SimulationFailedException

Throws:

InvalidInputException

DataNotFoundException

FileNotFoundException

IOException

SimulationFailedException

f

public final double[] f(double t,
                        double[] x)

Specified by:

f in interface odeToJava.modules.ODE

g

public final double[] g(double t,
                        double[] x)

Specified by:

g in interface odeToJava.modules.ODE

record

public final void record(double t,
                         double[] x)

Specified by:

record in interface odeToJava.modules.ODERecorder

initialize

public void initialize(Model pModel)
                throws DataNotFoundException

Throws:

DataNotFoundException

getDefaultSimulatorParameters

public SimulatorParameters getDefaultSimulatorParameters()

isStochasticSimulator

public boolean isStochasticSimulator()

Specified by:

isStochasticSimulator in class Simulator

checkSimulationParametersImpl

public void checkSimulationParametersImpl(SimulatorParameters pSimulatorParameters,
                                          int pNumResultsTimePoints)

Specified by:

checkSimulationParametersImpl in class Simulator