|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
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)
|
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |