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

P

paint(Graphics) - Method in class fern.tools.gnuplot.GnuPlot

PartialDerivativePropensityCalculator - Interface in fern.network

performReaction(int, int) - Method in interface fern.network.AmountManager

Reflects a (multiple) firing of a reaction by adjusting the populations of the reactants and the products.

performReaction(int, int) - Method in class fern.network.ConstantAmountManager

performReaction(int, int) - Method in class fern.network.DefaultAmountManager

Reflects a (multiple) firing of a reaction by adjusting the populations of the reactants and the products.

performStep(SimulationController) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

Performs a tau leaping step.

performStep(SimulationController) - Method in class fern.simulation.algorithm.CompositionRejection

performStep(SimulationController) - Method in class fern.simulation.algorithm.GibsonBruckSimulator

performStep(SimulationController) - Method in class fern.simulation.algorithm.GillespieEnhanced

performStep(SimulationController) - Method in class fern.simulation.algorithm.GillespieSimple

performStep(SimulationController) - Method in class fern.simulation.algorithm.HybridMaximalTimeStep

performStep(SimulationController) - Method in class fern.simulation.Simulator

Performs one simulation step.

plot() - Method in class fern.tools.gnuplot.GnuPlot

Calls gnuplot to plot the data.

present() - Method in class fern.benchmark.SimulatorCorrectness

Gets called after some iterations of the method benchmark in the base class.

present() - Method in class fern.benchmark.SimulatorFireTypes

Present results of this benchmark is gnuplot and text to stdout.

present() - Method in class fern.benchmark.SimulatorRandomNumbers

Present results of this benchmark is gnuplot and text to stdout.

present() - Method in class fern.benchmark.SimulatorTime

Present results of this benchmark is gnuplot and text to stdout.

print() - Method in class fern.simulation.observer.Observer

Gets called after the finish call and prints the results of this observer if a PrintWriter is registered.

Probability - Interface in fern.tools.functions

Function delegate for conditional probabilities.

Probability.Constant - Class in fern.tools.functions

Implementation that yields a constant (and hence independent) probability.

Probability.Constant(double) - Constructor for class fern.tools.functions.Probability.Constant

Probability.ReactionProbability - Class in fern.tools.functions

Implementation for the reaction probability for the autocatalytic network creation.

Probability.ReactionProbability(double, int) - Constructor for class fern.tools.functions.Probability.ReactionProbability

PropensityCalculator - Interface in fern.network

A PropensityCalculator is the way, a Network tells a Simulator how to calculate propensities for the reactions.

propensityChanged(int, double, double) - Method in class fern.simulation.algorithm.GroupContainer