Uses of Class
fern.simulation.Simulator

Packages that use Simulator

Package	Description
fern.benchmark
fern.example
fern.network
fern.network.sbml
fern.simulation.algorithm
fern.simulation.controller
fern.simulation.observer

Uses of Simulator in fern.benchmark

Methods in fern.benchmark that return Simulator

Modifier and Type	Method and Description
Simulator[]	SimulatorPerformance.getSimulators() Gets the simulators used by this benchmark.

Uses of Simulator in fern.example

Methods in fern.example that return Simulator

Modifier and Type	Method and Description
Simulator	HistogramDistanceTestSet.getSimulator()

Constructors in fern.example with parameters of type Simulator

Constructor and Description
CellGrowthObserver(Simulator sim, double generationTime, double timeOffset) Creates the observer for given simulator, generation time and a time offset (because the simulator starts at time 0 and for one example it actually starts at time 1000)
HistogramDistanceTestSet(Simulator sim, double eps, int runs, double time, String species)

Uses of Simulator in fern.network

Methods in fern.network with parameters of type Simulator

Modifier and Type	Method and Description
double	PropensityCalculator.calculatePropensity(int reaction, AmountManager amount, Simulator sim) Calculates the propensity for a reaction given the amounts of the AmountManager.
double	AbstractKineticConstantPropensityCalculator.calculatePropensity(int reaction, AmountManager amount, Simulator sim) Calculates the propensity for reaction by the formula h*c, where c is the kinetic constant for reaction and h is the number of distinct molecular reactant combinations for reaction.

Uses of Simulator in fern.network.sbml

Methods in fern.network.sbml with parameters of type Simulator

Modifier and Type	Method and Description
double	MathTree.calculate(AmountManager amount, Simulator sim) Evaluate the MathTree.
double	SBMLPropensityCalculator.calculatePropensity(int reaction, AmountManager amount, Simulator sim)
void	SBMLNetwork.registerEvents(Simulator sim) Registers the SBMLEventHandlerObserver for each event in the sbml file to the Simulator.
void	SBMLEventHandlerObserver.setSimulatorAsync(Simulator sim)

Constructors in fern.network.sbml with parameters of type Simulator

Constructor and Description
SBMLEventHandlerObserver(Simulator sim, SBMLNetwork net, SBMLinterpreter interpreter, org.sbml.jsbml.Event event) Creates the observer.

Uses of Simulator in fern.simulation.algorithm

Subclasses of Simulator in fern.simulation.algorithm

Modifier and Type	Class and Description
class	AbstractBaseTauLeaping Base class for all tau leaping procedures (which are different in the methods choosing the timestep candidates for critical and noncritical reactions).
class	AbstractTauLeapingPropensityBoundSimulator There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.
class	CompositionRejection This is an enhanced version of the original Direct method developed by Gillespie.
class	GibsonBruckSimulator Implementation of the algorithm of Gibson and Bruck.
class	GillespieEnhanced This is an enhanced version of the original Direct method developed by Gillespie.
class	GillespieSimple Implementation of Gillespie's Direct method.
class	HybridMaximalTimeStep This is an modified version of Maximal Time Step Method by Puchalka and Kierzec.
class	TauLeapingAbsoluteBoundSimulator There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.
class	TauLeapingRelativeBoundSimulator There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.
class	TauLeapingSpeciesPopulationBoundSimulator There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.

Constructors in fern.simulation.algorithm with parameters of type Simulator

Constructor and Description
GroupContainer(Simulator sim)

Uses of Simulator in fern.simulation.controller

Methods in fern.simulation.controller with parameters of type Simulator

Modifier and Type	Method and Description
boolean	DefaultController.goOn(Simulator sim)
boolean	SimulationController.goOn(Simulator sim) Returns whether or not to go on with the given simulation
boolean	OrController.goOn(Simulator sim)
boolean	AmountLowerThanController.goOn(Simulator sim)
boolean	AndController.goOn(Simulator sim)

Uses of Simulator in fern.simulation.observer

Methods in fern.simulation.observer that return Simulator

Modifier and Type	Method and Description
Simulator	Observer.getSimulator() Gets the simulator

Methods in fern.simulation.observer with parameters of type Simulator

Modifier and Type	Method and Description
boolean	AmountAtMomentObserver.goOn(Simulator sim) Causes the simulator to stop when theta has been passed and the amounts have been recorded.

Constructors in fern.simulation.observer with parameters of type Simulator

Constructor and Description
AmountAtMomentObserver(Simulator sim, double moment, int... speciesIndices) Creates the observer for the given simulator, the given theta and the given species
AmountAtMomentObserver(Simulator sim, double moment, String... speciesName) Creates the observer for the given simulator, the given theta and the given species
AmountIntervalObserver(Simulator sim, double interval, int... species) Creates the observer for a given simulator, a given interval and given species indices
AmountIntervalObserver(Simulator sim, double interval, int duration, String... speciesName) Creates the observer for a given simulator, a given interval and given species names with total simulation time.
AmountIntervalObserver(Simulator sim, double interval, String... speciesName) Creates the observer for a given simulator, a given interval and given species names.
FireTypeObserver(Simulator sim) Create the observer for the given simulator.
InstantOutputObserver(Simulator sim, PrintWriter pw) Creates the observer for a given simulator and a given PrintWriter
IntervalObserver(Simulator sim, double interval, int duration, String[] entityName)
IntervalObserver(Simulator sim, double interval, String[] entityName) Create the observer for a given simulator, a given interval, given indices with names.
LeapObserver(Simulator sim, String... speciesNames) Creates the observer with a given simulator and given species
MultiAmountIntervalObserver(Simulator sim, String presentationName, double interval, int... species) Creates the observer for a given simulator, a given interval and given species indices
MultiAmountIntervalObserver(Simulator sim, String presentationName, double interval, String... speciesName) Creates the observer for a given simulator, a given interval and given species names.
Observer(Simulator sim) Creates an observer dedicated to one simulator.
RandomNumberGeneratorCallObserver(Simulator sim) Creates the observer for the given simulator.
ReactionIntervalObserver(Simulator sim, double interval, int... reactions) Creates the observer for a given simulator, a given interval and given reaction indices.
ReactionIntervalObserver(Simulator sim, double interval, String... speciesNames) Creates the observer for a given simulator, a given interval and given neighbors.
TriggerObserver(Simulator sim)