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

S

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

Makes a copy of the amount array.

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

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

Makes a copy of the amount array.

saveData(File) - Method in class fern.tools.gnuplot.GnuPlot

Saves the gnuplot data to one ore more files.

saveHistogram(Map<Integer, Integer>, File) - Static method in class fern.tools.NumberTools

Writes a histogram to a file.

saveImage(File) - Method in class fern.tools.gnuplot.GnuPlot

Saves the plotted data to a png file.

saveToFile(File) - Method in class fern.network.fernml.FernMLNetwork

Saves the actual FernMLNetwork to a file.

saveToFile(File) - Method in class fern.network.sbml.SBMLNetwork

Saves the current SBMLNetwork to a file.

saveToFile(File, long, long) - Method in class fern.network.sbml.SBMLNetwork

Saves the current SBMLNetwork to a sbml file with given level and version.

SBaseAdded(PluginSBase) - Method in class fern.cellDesigner.FernCellDesignerPlugin

SBaseChanged(PluginSBase) - Method in class fern.cellDesigner.FernCellDesignerPlugin

SBaseDeleted(PluginSBase) - Method in class fern.cellDesigner.FernCellDesignerPlugin

SBMLEventHandlerObserver - Class in fern.network.sbml

Observer which handles an event of a sbml model.

SBMLEventHandlerObserver(Simulator, SBMLNetwork, Event) - Constructor for class fern.network.sbml.SBMLEventHandlerObserver

Creates the observer.

SBMLMathTreeTest - Class in fern.example

SBMLMathTreeTest() - Constructor for class fern.example.SBMLMathTreeTest

SBMLNetwork - Class in fern.network.sbml

For specifications of the sbml format refer to http:\\www.sbml.org.

SBMLNetwork(File) - Constructor for class fern.network.sbml.SBMLNetwork

Creates a network from a sbmlfile.

SBMLNetwork(File, boolean) - Constructor for class fern.network.sbml.SBMLNetwork

Creates a network from a sbml file.

SBMLNetwork(Network) - Constructor for class fern.network.sbml.SBMLNetwork

Create a SBMLNetwork from an existing Network.

SBMLPropensityCalculator - Class in fern.network.sbml

Propensity calculator which is used for SBMLNetworks.

SBMLPropensityCalculator(SBMLNetwork) - Constructor for class fern.network.sbml.SBMLPropensityCalculator

Creates the MathTrees and parses the parameters.

search(IntSearchStructure, int[], int[], NetworkSearchAction) - Method in class fern.analysis.AnalysisBase

Performs a search starting at the given sources (which means the contents of speciesSource and reactionSource are the initial content of the search structure IntSearchStructure.

sep - Static variable in class fern.cellDesigner.ui.ExtendedPane

sep - Static variable in class fern.cytoscape.ui.ExtendedPane

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

Sets the current amount of a species.

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

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

Sets the current amount of a species.

setAmount(int, long) - Method in class fern.simulation.algorithm.GibsonBruckSimulator

setAmount(int, long) - Method in class fern.simulation.algorithm.GillespieEnhanced

setAmount(int, long) - Method in class fern.simulation.algorithm.HybridMaximalTimeStep

setAmount(int, long) - Method in class fern.simulation.Simulator

Sets the amount of the given species.

setAmountBottomColor(Color) - Method in class fern.cytoscape.ColorCalculator

setAmountTopColor(Color) - Method in class fern.cytoscape.ColorCalculator

setAttributes(NetworkChecker) - Method in class fern.cytoscape.ui.ExtendedPane

setCatalyzedKineticConstant(double) - Method in class fern.network.creation.AutocatalyticNetwork

Sets the kinetic constant for catalyzed reactions.

setConstant(int, double) - Method in class fern.network.ArrayKineticConstantPropensityCalculator

setCountGenerations(boolean) - Method in class fern.tools.Stochastics

Sets whether or not to count the number of random number generations

setDefaultStyle(String) - Method in class fern.tools.gnuplot.GnuPlot

The defaultStyle is used, when no style is defined for an column in an axes object.

setEfficientlyAdaptSum(boolean) - Method in class fern.simulation.algorithm.GillespieEnhanced

setEnabled(boolean) - Method in class fern.cellDesigner.ui.ExtendedPane

setEnabled(boolean) - Method in class fern.cellDesigner.ui.OverviewPane

setEnabled(boolean) - Method in class fern.cytoscape.ui.ExtendedPane

setEnabled(boolean) - Method in class fern.cytoscape.ui.OverviewPane

setEnabledTauLeaping(boolean) - Method in class fern.cellDesigner.ui.ExtendedPane

setEnabledTauLeaping(boolean) - Method in class fern.cytoscape.ui.ExtendedPane

setEpsilon(double) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

The epsilon is an error control parameter and bounds the expected change of the propensity functions by epsilon * a_sum.

setErrorMessage(Network, String) - Method in class fern.cellDesigner.ui.OverviewPane

setErrorMessage(Network, String) - Method in class fern.cytoscape.ui.OverviewPane

setInitialAmount(int, long) - Method in class fern.cellDesigner.CellDesignerNetworkWrapper

setInitialAmount(int, long) - Method in class fern.cytoscape.CytoscapeNetworkWrapper

setInitialAmount(int, long) - Method in class fern.network.creation.AutocatalyticNetwork

setInitialAmount(int, long) - Method in class fern.network.fernml.FernMLNetwork

setInitialAmount(int, long) - Method in class fern.network.modification.ExtractSubNetwork

setInitialAmount(int, long) - Method in class fern.network.modification.ModifierNetwork

setInitialAmount(int, long) - Method in interface fern.network.Network

Sets the initial amount of the specified molecule species.

setInitialAmount(int, long) - Method in class fern.network.sbml.SBMLNetwork

setInterpolateTheta(boolean) - Method in class fern.simulation.Simulator

Sets whether the amount values are returned interpolated for theta events.

setLabel(int, String) - Method in class fern.tools.gnuplot.Axes

Sets the label for a column.

setLabelFormat(String) - Method in class fern.simulation.observer.Observer

Sets the label format for Observer.getLabel(String).

setLangevinThreshold(double) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

The Langevin threshold determines, when the normal distribution is used as an approximation for the poisson distribution.

setMonomerAmount(long) - Method in class fern.network.creation.AutocatalyticNetwork

Sets the initial amount of the monomers for a simulation algorithm.

setNCritical(int) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

The nCritical determines, when a reaction is called critical.

setNetworkAnnotation(String, String) - Method in class fern.cytoscape.CytoscapeAnnotationManager

setNetworkAnnotation(String, String) - Method in interface fern.network.AnnotationManager

Sets the network annotation of the specified field.

setNetworkAnnotation(String, String) - Method in class fern.network.AnnotationManagerImpl

setNetworkAnnotation(String, String) - Method in class fern.network.fernml.FernMLAnnotationManager

setNetworkChecker(NetworkChecker) - Method in class fern.cytoscape.FernVisualStyle

setNumBins(int) - Method in class fern.benchmark.Benchmark

Sets the number of bins that are used for creating gnuplot histograms.

setNumSimpleCalls(int) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

The numSimpleCalls determines, how often the SSA is called, when tau leaping is abandoned.

setOtherAmount(long) - Method in class fern.network.creation.AutocatalyticNetwork

Sets the initial amount of the not-monomers for a simulation algorithm.

setPlotQuality(boolean) - Method in class fern.simulation.observer.IntervalObserver

Sets whether or not to plot quality data.

setPrintWriter(PrintWriter) - Method in class fern.simulation.observer.Observer

Registers a PrintWriter

setReactionAnnotation(int, String, String) - Method in class fern.cytoscape.CytoscapeAnnotationManager

setReactionAnnotation(int, String, String) - Method in interface fern.network.AnnotationManager

Sets the reaction annotation of the specified field.

setReactionAnnotation(int, String, String) - Method in class fern.network.AnnotationManagerImpl

setReactionAnnotation(int, String, String) - Method in class fern.network.fernml.FernMLAnnotationManager

setReactionColor(Color) - Method in class fern.cytoscape.ColorCalculator

setReactionFire(Node) - Method in class fern.cytoscape.FernVisualStyle

setReactionUnFire(Node) - Method in class fern.cytoscape.FernVisualStyle

setRecordStart(double) - Method in class fern.simulation.observer.ReactionIntervalObserver

Sets the moment in time where the recording starts

setScale(ColorCalculator.Scale) - Method in class fern.cytoscape.ColorCalculator

setScaleMax(double) - Method in class fern.cytoscape.ColorCalculator

setSeed(long) - Method in class fern.tools.Stochastics

Sets a new seed for the random number generator.

setSeed(Date) - Method in class fern.tools.Stochastics

Sets a new seed for the random number generator.

setShowSteps(int) - Method in class fern.benchmark.SimulatorPerformance

Sets the number of iterations between two present-calls.

setSimulatorAsync(Simulator) - Method in class fern.network.sbml.SBMLEventHandlerObserver

setSpecies(Network) - Method in class fern.cellDesigner.ui.ExtendedPane

setSpecies(Network) - Method in class fern.cytoscape.ui.ExtendedPane

setSpeciesAnnotation(int, String, String) - Method in class fern.cytoscape.CytoscapeAnnotationManager

setSpeciesAnnotation(int, String, String) - Method in interface fern.network.AnnotationManager

Sets the species annotation of the specified field.

setSpeciesAnnotation(int, String, String) - Method in class fern.network.AnnotationManagerImpl

setSpeciesAnnotation(int, String, String) - Method in class fern.network.fernml.FernMLAnnotationManager

setSpeciesInitialAmount(Node, long) - Method in class fern.cytoscape.NetworkChecker.NodeParameter

setStyle(int, String) - Method in class fern.tools.gnuplot.Axes

Sets the style for a column.

setTheta(double) - Method in class fern.simulation.observer.Observer

Sets the moment in time, where the simulator has to invoke Observer.theta(double).

setThetaMethod(boolean) - Method in class fern.simulation.observer.IntervalObserver

Using theta method means that the time intervals are registered at the simulator and the simulator invokes at this moment the method theta.

setTime(double) - Method in class fern.simulation.controller.DefaultController

Sets the time where the simulation has to stop.

setUncatalyzedKineticConstant(double) - Method in class fern.network.creation.AutocatalyticNetwork

Sets the kinetic constant for not catalyzed reactions.

setUseSimpleFactor(double) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

The useSimpleFactor determines, when the tau leaping is abandoned and the SSA method is used (if tausetValue(Node, double, double) - Method in class fern.cytoscape.FernVisualStyle

setVerbose(boolean) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

Sets if each step is to print to stdout.

setVolume(double) - Method in class fern.simulation.algorithm.GibsonBruckSimulator

setVolume(double) - Method in class fern.simulation.algorithm.GillespieEnhanced

setVolume(double) - Method in class fern.simulation.algorithm.HybridMaximalTimeStep

setVolume(double) - Method in class fern.simulation.Simulator

Sets the volume of the reaction network.

ShortestPath - Class in fern.analysis

Computes shortest paths in the network by a bfs.

ShortestPath(Network) - Constructor for class fern.analysis.ShortestPath

Creates the class with the specified network.

ShortestPath.Path - Class in fern.analysis

Encapsulates a path from one species to another.

ShortestPath.Path(int[]) - Constructor for class fern.analysis.ShortestPath.Path

Creates a path from an array.

shuffle(int[]) - Static method in class fern.tools.NumberTools

Shuffles the content of the given array.

SimulationController - Interface in fern.simulation.controller

Simulators are controlled by implementing classes.

Simulator - Class in fern.simulation

Base class for stochastic simulators.

Simulator(Network) - Constructor for class fern.simulation.Simulator

Creates a new simulator for the given network.

Simulator.FireType - Enum in fern.simulation

Defines different types of a firing for reactions.

SimulatorCorrectness - Class in fern.benchmark

Benchmark the correctness of the built-in simulators for a given net.

SimulatorCorrectness(Network, double, String...) - Constructor for class fern.benchmark.SimulatorCorrectness

Creates the benchmark instance with given network, moment in time and species.

SimulatorFireTypes - Class in fern.benchmark

Benchmark the Simulator.FireTypes for a given net.

SimulatorFireTypes(Network, double) - Constructor for class fern.benchmark.SimulatorFireTypes

Create the benchmark and defines the time each simulator has to run in one iteration.

SimulatorPerformance - Class in fern.benchmark

Measures the performance of the different simulation algorithms for a given network.

SimulatorPerformance(Network) - Constructor for class fern.benchmark.SimulatorPerformance

Registers the six built-in simulators for the performance benchmarks.

SimulatorRandomNumbers - Class in fern.benchmark

Check the number of random number creations of different distributions for a given net.

SimulatorRandomNumbers(Network, double) - Constructor for class fern.benchmark.SimulatorRandomNumbers

Create the benchmark and defines the time each simulator has to run in one iteration.

SimulatorTime - Class in fern.benchmark

SimulatorTime(Network, double) - Constructor for class fern.benchmark.SimulatorTime

Create the benchmark and defines the time each simulator has to run in one iteration.

size() - Method in class fern.simulation.algorithm.IndexedPriorityQueue

Gets the number of nodes in the binary heap.

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

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

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

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

start() - Method in class fern.benchmark.Benchmark

sets a start time for the benchmark system

start(double) - Method in class fern.simulation.Simulator

Starts the simulation up to a given time.

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

Start the simulation with the given SimulationController.

Start - Class in fern

Start() - Constructor for class fern.Start

started() - Method in class fern.cytoscape.CytoscapeColorChangeObserver

started() - Method in class fern.example.CellGrowthObserver

started() - Method in class fern.network.sbml.SBMLEventHandlerObserver

started() - Method in class fern.simulation.observer.AmountAtMomentObserver

Register theta at the simulator.

started() - Method in class fern.simulation.observer.FireTypeObserver

Do nothing.

started() - Method in class fern.simulation.observer.InstantOutputObserver

Prints event.

started() - Method in class fern.simulation.observer.IntervalObserver

Clears the recorded values and registers (if needed) theta

started() - Method in class fern.simulation.observer.LeapObserver

Clears the recorded data.

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

Gets called when the simulation has started after the initialization and before the termination condition is checked the first time.

started() - Method in class fern.simulation.observer.RandomNumberGeneratorCallObserver

Resets the count variables of the random number generator calls.

started() - Method in class fern.simulation.observer.ReactionIntervalObserver

stddev(double[]) - Static method in class fern.tools.NumberTools

Gets the standard deviation of the array

step() - Method in class fern.cytoscape.CytoscapeColorChangeObserver

step() - Method in class fern.example.CellGrowthObserver

step() - Method in class fern.network.sbml.SBMLEventHandlerObserver

step() - Method in class fern.simulation.observer.AmountAtMomentObserver

Do nothing.

step() - Method in class fern.simulation.observer.FireTypeObserver

Do nothing.

step() - Method in class fern.simulation.observer.InstantOutputObserver

Prints event.

step() - Method in class fern.simulation.observer.IntervalObserver

If the step method is used, the data is recorded here.

step() - Method in class fern.simulation.observer.LeapObserver

Record the time and amounts of the species.

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

Gets called after each termination check and before Simulator.performStep(fern.simulation.controller.SimulationController) is called.

step() - Method in class fern.simulation.observer.RandomNumberGeneratorCallObserver

Do nothing.

Stochastics - Class in fern.tools

Manages a random number generators for various distributions.

sum(int[]) - Static method in class fern.tools.NumberTools

Gets the sum of the values in the array.