org.systemsbiology.chem
Class Simulator

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

Direct Known Subclasses:

SimulatorDeterministicBase, SimulatorOdeToJavaBase, SimulatorStochasticBase

public abstract class Simulator

extends Object

Base class extended by all classes implementing ISimulator. This class contains a lot of methods and fields of common use to all simulator classes. From the standpoint of object-oriented correctness, this really should be done by composition rather than inheritance. For performance, accessor methods are avoided in favor of direct field access by subclasses.

Author:

sramsey

Field Summary

protected static long	DEFAULT_MIN_NUM_MILLISECONDS_FOR_UPDATE
protected DelayedReactionSolver[]	mDelayedReactionSolvers
protected Object[]	mDynamicSymbolAdjustmentVectors
protected String[]	mDynamicSymbolNames
protected Species[]	mDynamicSymbols
protected double[]	mDynamicSymbolValues
protected double[]	mInitialDynamicSymbolValues
protected boolean	mInitialized
protected boolean	mIsStochasticSimulator
protected long	mMinNumMillisecondsForUpdate
protected String	mModelName
protected Value[]	mNonDynamicSymbolExpressionValues
protected Value[]	mNonDynamicSymbolValues
protected double[]	mReactionProbabilities
protected Value[]	mReactionRates
protected Reaction[]	mReactions
protected DelayedReactionSolver[]	mReactionsDelayedReactionAssociations
protected HashMap[]	mReactionsLocalParamSymbolsMaps
protected Object[]	mReactionsProductsDynamic
protected Object[]	mReactionsProductsSpecies
protected Object[]	mReactionsProductsStoichiometries
protected Object[]	mReactionsReactantsDynamic
protected Object[]	mReactionsReactantsSpecies
protected Object[]	mReactionsReactantsStoichiometries
protected Symbol[]	mReactionSymbols
protected SimulationController	mSimulationController
protected SimulationProgressReporter	mSimulationProgressReporter
protected SymbolEvaluatorChem	mSymbolEvaluator
protected HashMap	mSymbolMap
protected boolean	mUseExpressionValueCaching
protected static int	NULL_REACTION

Constructor Summary

Simulator()

Method Summary

protected int	addRequestedSymbolValues(double pCurTime, int pLastTimeIndex, Symbol[] pRequestedSymbols, double[] pTimeValues, Object[] pRetSymbolValues)
boolean	canComputeFluctuations()
void	checkSimulationParameters(double pStartTime, double pEndTime, SimulatorParameters pSimulatorParameters, int pNumResultsTimePoints)
protected void	checkSimulationParametersForDeterministicSimulator(SimulatorParameters pSimulatorParameters, int pNumResultsTimePoints)
protected abstract void	checkSimulationParametersImpl(SimulatorParameters pSimulatorParameters, int pNumResultsTimePoints)
protected void	clearExpressionValueCaches()
protected void	clearSimulatorState()
protected void	computeDerivative(double[] pTempDynamicSymbolValues, double[] pDynamicSymbolDerivatives)
protected Expression	computeRatePartialDerivativeExpression(int pReactionCtr, Expression pRateExpression, SymbolValue pSymbolValue, SymbolEvaluatorChem pSymbolEvaluator)
protected void	computeReactionProbabilities()
protected Symbol[]	createRequestedSymbolArray(HashMap pSymbolMap, String[] pRequestedSymbols)
protected SimulationResults	createSimulationResults(double pStartTime, double pEndTime, SimulatorParameters pSimulatorParameters, String[] pResultsSymbolNames, double[] pResultsTimeValues, Object[] pResultsSymbolValues, double[] pResultsFinalSymbolFluctuations)
protected static double[]	createTimesArray(double pStartTime, double pEndTime, int pNumTimePoints)
abstract String	getAlias()
protected static double	getDelayedReactionEstimatedAverageFutureRate(SymbolEvaluatorChem pSymbolEvaluator, DelayedReactionSolver[] pDelayedReactionSolvers)
protected double	getMinDelayedReactionDelay()
static Expression[]	getReactionRateExpressions(Reaction[] pReactions)
protected boolean	hasDelayedReactionSolvers()
protected void	initializeDynamicSymbolAdjustmentVectors()
protected void	initializeSimulator(Model pModel)
boolean	isInitialized()
abstract boolean	isStochasticSimulator()
protected void	prepareForSimulation(double pStartTime)
protected void	resizeDelayedReactionSolvers(int pNumHistoryBins)
void	setController(SimulationController pSimulationController)
protected void	setInitialized(boolean pInitialized)
protected void	setMinNumMillisecondsForUpdate(long pMinNumMillisecondsForUpdate)
void	setProgressReporter(SimulationProgressReporter pSimulationProgressReporter)
void	setStatusUpdateIntervalSeconds(double pUpdateIntervalSeconds)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_MIN_NUM_MILLISECONDS_FOR_UPDATE

protected static final long DEFAULT_MIN_NUM_MILLISECONDS_FOR_UPDATE

See Also:

Constant Field Values

NULL_REACTION

protected static final int NULL_REACTION

See Also:

Constant Field Values

mModelName

protected String mModelName

mNonDynamicSymbolValues

protected Value[] mNonDynamicSymbolValues

mNonDynamicSymbolExpressionValues

protected Value[] mNonDynamicSymbolExpressionValues

mUseExpressionValueCaching

protected boolean mUseExpressionValueCaching

mSymbolEvaluator

protected SymbolEvaluatorChem mSymbolEvaluator

mSymbolMap

protected HashMap mSymbolMap

mSimulationController

protected SimulationController mSimulationController

mDelayedReactionSolvers

protected DelayedReactionSolver[] mDelayedReactionSolvers

mInitialized

protected boolean mInitialized

mMinNumMillisecondsForUpdate

protected long mMinNumMillisecondsForUpdate

mSimulationProgressReporter

protected SimulationProgressReporter mSimulationProgressReporter

mIsStochasticSimulator

protected boolean mIsStochasticSimulator

mDynamicSymbols

protected Species[] mDynamicSymbols

mInitialDynamicSymbolValues

protected double[] mInitialDynamicSymbolValues

mDynamicSymbolNames

protected String[] mDynamicSymbolNames

mDynamicSymbolValues

protected double[] mDynamicSymbolValues

mReactions

protected Reaction[] mReactions

mDynamicSymbolAdjustmentVectors

protected Object[] mDynamicSymbolAdjustmentVectors

mReactionProbabilities

protected double[] mReactionProbabilities

mReactionsReactantsSpecies

protected Object[] mReactionsReactantsSpecies

mReactionsReactantsStoichiometries

protected Object[] mReactionsReactantsStoichiometries

mReactionsReactantsDynamic

protected Object[] mReactionsReactantsDynamic

mReactionsProductsSpecies

protected Object[] mReactionsProductsSpecies

mReactionsProductsStoichiometries

protected Object[] mReactionsProductsStoichiometries

mReactionsProductsDynamic

protected Object[] mReactionsProductsDynamic

mReactionsLocalParamSymbolsMaps

protected HashMap[] mReactionsLocalParamSymbolsMaps

mReactionRates

protected Value[] mReactionRates

mReactionsDelayedReactionAssociations

protected DelayedReactionSolver[] mReactionsDelayedReactionAssociations

mReactionSymbols

protected Symbol[] mReactionSymbols

Constructor Detail

Simulator

public Simulator()

Method Detail

hasDelayedReactionSolvers

protected boolean hasDelayedReactionSolvers()

isInitialized

public final boolean isInitialized()

canComputeFluctuations

public boolean canComputeFluctuations()

resizeDelayedReactionSolvers

protected final void resizeDelayedReactionSolvers(int pNumHistoryBins)

prepareForSimulation

protected final void prepareForSimulation(double pStartTime)

isStochasticSimulator

public abstract boolean isStochasticSimulator()

initializeSimulator

protected final void initializeSimulator(Model pModel)
                                  throws DataNotFoundException

Throws:

DataNotFoundException

setInitialized

protected void setInitialized(boolean pInitialized)

clearSimulatorState

protected void clearSimulatorState()

initializeDynamicSymbolAdjustmentVectors

protected final void initializeDynamicSymbolAdjustmentVectors()

getAlias

public abstract String getAlias()

createSimulationResults

protected final SimulationResults createSimulationResults(double pStartTime,
                                                          double pEndTime,
                                                          SimulatorParameters pSimulatorParameters,
                                                          String[] pResultsSymbolNames,
                                                          double[] pResultsTimeValues,
                                                          Object[] pResultsSymbolValues,
                                                          double[] pResultsFinalSymbolFluctuations)

addRequestedSymbolValues

protected final int addRequestedSymbolValues(double pCurTime,
                                             int pLastTimeIndex,
                                             Symbol[] pRequestedSymbols,
                                             double[] pTimeValues,
                                             Object[] pRetSymbolValues)
                                      throws DataNotFoundException

Throws:

DataNotFoundException

createTimesArray

protected static final double[] createTimesArray(double pStartTime,
                                                 double pEndTime,
                                                 int pNumTimePoints)

createRequestedSymbolArray

protected final Symbol[] createRequestedSymbolArray(HashMap pSymbolMap,
                                                    String[] pRequestedSymbols)
                                             throws DataNotFoundException

Throws:

DataNotFoundException

checkSimulationParameters

public final void checkSimulationParameters(double pStartTime,
                                            double pEndTime,
                                            SimulatorParameters pSimulatorParameters,
                                            int pNumResultsTimePoints)
                                     throws IllegalArgumentException,
                                            IllegalStateException

Throws:

IllegalArgumentException

IllegalStateException

checkSimulationParametersImpl

protected abstract void checkSimulationParametersImpl(SimulatorParameters pSimulatorParameters,
                                                      int pNumResultsTimePoints)

computeReactionProbabilities

protected final void computeReactionProbabilities()
                                           throws DataNotFoundException

Throws:

DataNotFoundException

getDelayedReactionEstimatedAverageFutureRate

protected static final double getDelayedReactionEstimatedAverageFutureRate(SymbolEvaluatorChem pSymbolEvaluator,
                                                                           DelayedReactionSolver[] pDelayedReactionSolvers)
                                                                    throws DataNotFoundException

Throws:

DataNotFoundException

clearExpressionValueCaches

protected final void clearExpressionValueCaches()

computeDerivative

protected final void computeDerivative(double[] pTempDynamicSymbolValues,
                                       double[] pDynamicSymbolDerivatives)
                                throws DataNotFoundException

Throws:

DataNotFoundException

setProgressReporter

public final void setProgressReporter(SimulationProgressReporter pSimulationProgressReporter)

setController

public final void setController(SimulationController pSimulationController)

setStatusUpdateIntervalSeconds

public final void setStatusUpdateIntervalSeconds(double pUpdateIntervalSeconds)
                                          throws IllegalArgumentException

Throws:

IllegalArgumentException

setMinNumMillisecondsForUpdate

protected final void setMinNumMillisecondsForUpdate(long pMinNumMillisecondsForUpdate)

getMinDelayedReactionDelay

protected final double getMinDelayedReactionDelay()

computeRatePartialDerivativeExpression

protected Expression computeRatePartialDerivativeExpression(int pReactionCtr,
                                                            Expression pRateExpression,
                                                            SymbolValue pSymbolValue,
                                                            SymbolEvaluatorChem pSymbolEvaluator)
                                                     throws DataNotFoundException

Throws:

DataNotFoundException

getReactionRateExpressions

public static Expression[] getReactionRateExpressions(Reaction[] pReactions)
                                               throws DataNotFoundException

Throws:

DataNotFoundException

checkSimulationParametersForDeterministicSimulator

protected void checkSimulationParametersForDeterministicSimulator(SimulatorParameters pSimulatorParameters,
                                                                  int pNumResultsTimePoints)