Uses of Class
fern.simulation.Simulator

Packages that use Simulator
fern.benchmark Provides classes for benchmarking simulations (time benchmarks, histogram distance calculation). 
fern.cellDesigner   
fern.cellDesigner.ui   
fern.cytoscape Provides the classes for the cytoscape plugin. 
fern.cytoscape.ui   
fern.example Contains examples and demonstrations of the framework. 
fern.network Provides general classes and interfaces for storing network data. 
fern.network.sbml Provides the classes for parsing and using sbml based networks. 
fern.simulation.algorithm Provides algorithms for stochastic simultion of reaction networks. 
fern.simulation.controller Provides classes to control the simulations. 
fern.simulation.observer Provides classes to observe certain aspects of simulations. 
 

Uses of Simulator in fern.benchmark
 

Methods in fern.benchmark that return Simulator
 Simulator[] SimulatorPerformance.getSimulators()
          Gets the simulators used by this benchmark.
 

Uses of Simulator in fern.cellDesigner
 

Methods in fern.cellDesigner with parameters of type Simulator
 double CellDesignerPropensityCalculator.calculatePropensity(int reaction, AmountManager amount, Simulator sim)
           
 

Uses of Simulator in fern.cellDesigner.ui
 

Methods in fern.cellDesigner.ui that return Simulator
 Simulator OverviewPane.getSimulator()
           
 

Uses of Simulator in fern.cytoscape
 

Constructors in fern.cytoscape with parameters of type Simulator
CytoscapeColorChangeObserver(boolean visualize, boolean showTrendSteps, Simulator sim, CytoscapeNetworkWrapper net, FernVisualStyle style, String[] trendSpecies, double time)
           
 

Uses of Simulator in fern.cytoscape.ui
 

Methods in fern.cytoscape.ui that return Simulator
 Simulator OverviewPane.getSimulator()
           
 

Uses of Simulator in fern.example
 

Methods in fern.example that return Simulator
 Simulator HistogramDistanceTestSet.getSimulator()
           
 

Constructors in fern.example with parameters of type Simulator
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
 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.
 double PropensityCalculator.calculatePropensity(int reaction, AmountManager amount, Simulator sim)
          Calculates the propensity for a reaction given the amounts of the AmountManager.
 

Uses of Simulator in fern.network.sbml
 

Methods in fern.network.sbml with parameters of type Simulator
 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
SBMLEventHandlerObserver(Simulator sim, SBMLNetwork net, org.sbml.libsbml.Event event)
          Creates the observer.
 

Uses of Simulator in fern.simulation.algorithm
 

Subclasses of Simulator in fern.simulation.algorithm
 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
GroupContainer(Simulator sim)
           
 

Uses of Simulator in fern.simulation.controller
 

Methods in fern.simulation.controller with parameters of type Simulator
 boolean AmountLowerThanController.goOn(Simulator sim)
           
 boolean OrController.goOn(Simulator sim)
           
 boolean AndController.goOn(Simulator sim)
           
 boolean SimulationController.goOn(Simulator sim)
          Returns whether or not to go on with the given simulation
 boolean DefaultController.goOn(Simulator sim)
           
 

Uses of Simulator in fern.simulation.observer
 

Methods in fern.simulation.observer that return Simulator
 Simulator Observer.getSimulator()
          Gets the simulator
 

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