A B C D E F G H I J K L M N O P R S T U V

R

RandomNumber - Class in fern.benchmark

Benchmarking of the time needed for different random number generations.

RandomNumber() - Constructor for class fern.benchmark.RandomNumber

RandomNumberGeneratorCallObserver - Class in fern.simulation.observer

Observes the calls to the random number generator and count the number of drawn random number of different distributions.

RandomNumberGeneratorCallObserver(Simulator) - Constructor for class fern.simulation.observer.RandomNumberGeneratorCallObserver

Creates the observer for the given simulator.

reactionDiscovered(int) - Method in interface fern.analysis.NetworkSearchAction

Gets called when a reaction is inserted into the search structure.

reactionFinished(int) - Method in interface fern.analysis.NetworkSearchAction

Gets called when a reaction gets out of the search structure.

ReactionIntervalObserver - Class in fern.simulation.observer

Observes number of firings of reactions repeatedly after certain intervals.

ReactionIntervalObserver(Simulator, double, String...) - Constructor for class fern.simulation.observer.ReactionIntervalObserver

Creates the observer for a given simulator, a given interval and given neighbors.

ReactionIntervalObserver(Simulator, double, int...) - Constructor for class fern.simulation.observer.ReactionIntervalObserver

Creates the observer for a given simulator, a given interval and given reaction indices.

readNetwork(File) - Static method in class fern.network.NetworkLoader

Tries to read the given file and returns the network in it (if there is one)

registerEvents(Simulator) - Method in class fern.network.sbml.SBMLNetwork

Registers the SBMLEventHandlerObserver for each event in the sbml file to the Simulator.

registerNewTheta(Observer, double) - Method in class fern.simulation.Simulator

Is called by Observer.setTheta(double).

reinitialize() - Method in class fern.simulation.algorithm.CompositionRejection

reinitialize() - Method in class fern.simulation.algorithm.GibsonBruckSimulator

reinitialize() - Method in class fern.simulation.algorithm.GillespieEnhanced

reinitialize() - Method in class fern.simulation.algorithm.GillespieSimple

reinitialize() - Method in class fern.simulation.algorithm.HybridMaximalTimeStep

reinitialize() - Method in class fern.simulation.Simulator

Reset propensities when a event has been executed.

reloadNetwork() - Method in class fern.cellDesigner.ui.MainFrame

reloadNetwork(NetworkChecker) - Method in class fern.cytoscape.ui.MainFrame

reloadNetworkByButton() - Method in class fern.cytoscape.ui.MainFrame

resetAmount() - Method in interface fern.network.AmountManager

Resets the amount of each species to the initial amount retrieved by the networks AnnotationManager.

resetAmount() - Method in class fern.network.ConstantAmountManager

resetAmount() - Method in class fern.network.DefaultAmountManager

Resets the amount of each species to the initial amount retrieved by the networks AnnotationManager.

resetColors() - Method in class fern.cytoscape.FernVisualStyle

resetCounts() - Method in class fern.tools.Stochastics

Resets the counts for each distribution to zero.

resetSeed() - Method in class fern.tools.Stochastics

Sets the seed to the current date

REVERSIBLE_SUFFIX - Static variable in class fern.network.modification.ReversibleNetwork

Suffix which marks annotations for virtually created reverse reactions.

ReversibleNetwork - Class in fern.network.modification

Doubles each reaction in a way that each original unidirectional reaction becomes reversible.As proposed by ModifierNetwork, the reactions are not copied but the indices are redirected.

ReversibleNetwork(Network, PropensityCalculator) - Constructor for class fern.network.modification.ReversibleNetwork

Creates a new network from an original network and virtually creates for each reaction a new inverse reaction.

RND - Static variable in class fern.simulation.algorithm.IndexedPriorityQueue

rollback() - Method in interface fern.network.AmountManager

Restore the amount array from the recently saved one.

rollback() - Method in class fern.network.ConstantAmountManager

rollback() - Method in class fern.network.DefaultAmountManager

Restore the amount array from the recently saved one.