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

A

AbstractBaseTauLeaping - Class in fern.simulation.algorithm

Base class for all tau leaping procedures (which are different in the methods choosing the timestep candidates for critical and noncritical reactions).

AbstractBaseTauLeaping(Network) - Constructor for class fern.simulation.algorithm.AbstractBaseTauLeaping

Create the simulator for a given network.

AbstractKineticConstantPropensityCalculator - Class in fern.network

Base implementation of a PropensityCalculator.

AbstractKineticConstantPropensityCalculator(int[][]) - Constructor for class fern.network.AbstractKineticConstantPropensityCalculator

Creates a AbstractKineticConstantPropensityCalculator by an array of adjacency arrays for the reaction's reactant species (which are the only one needed for the propensity calculation).

AbstractNetworkImpl - Class in fern.network

Base implementation for the Network interface.

AbstractNetworkImpl(String) - Constructor for class fern.network.AbstractNetworkImpl

Create the network and give it an identifier.

AbstractTauLeapingPropensityBoundSimulator - Class in fern.simulation.algorithm

There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.

AbstractTauLeapingPropensityBoundSimulator(Network) - Constructor for class fern.simulation.algorithm.AbstractTauLeapingPropensityBoundSimulator

actionPerformed(ActionEvent) - Method in class fern.cytoscape.CytoscapeVisualizer.ShowMainFrameAction

actionPerformed(ActionEvent) - Method in class fern.cytoscape.CytoscapeVisualizer.SimulationAction

activateReaction(int, double, Simulator.FireType, int) - Method in class fern.cytoscape.CytoscapeColorChangeObserver

activateReaction(int, double, Simulator.FireType, int) - Method in class fern.example.CellGrowthObserver

activateReaction(int, double, Simulator.FireType, int) - Method in class fern.network.sbml.SBMLEventHandlerObserver

activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.AmountAtMomentObserver

Do nothing

activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.FireTypeObserver

Counts the firing for the given Simulator.FireType

activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.InstantOutputObserver

Prints event.

activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.IntervalObserver

Do nothing.

activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.LeapObserver

Do nothing.

activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.Observer

Gets called before a reaction fires.

activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.RandomNumberGeneratorCallObserver

Do nothing.

activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.ReactionIntervalObserver

Record the firing of mu, if mu is registered.

add(int) - Method in interface fern.analysis.IntSearchStructure

addAxes(Axes) - Method in class fern.tools.gnuplot.Axes

Attaches an Axes object to this one.

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

Adds commands to the list of commands which are given to gnuplot by invoking plot

addData(double[]) - Method in class fern.benchmark.Benchmark

Adds benchmark data to the data pool.

addData(Collection, String[], String[]) - Method in class fern.tools.gnuplot.GnuPlot

Adds data in order to plot it.

addData(Axes) - Method in class fern.tools.gnuplot.GnuPlot

Adds data in order to plot it.

addData(Object, String[], String[]) - Method in class fern.tools.gnuplot.GnuPlot

Adds data in order to plot it.

addData(Object[], boolean, String[], String[]) - Method in class fern.tools.gnuplot.GnuPlot

Adds data in order to plot it.

Additional - Static variable in class fern.tools.gnuplot.Axes

addObserver(Observer) - Method in class fern.simulation.Simulator

Adds an observer to the list of observers.

addPluginMenu() - Method in class fern.cellDesigner.FernCellDesignerPlugin

addTypesToFileChooser(JFileChooser) - Static method in class fern.network.NetworkLoader

Adds available types of networks to a JFileChooser.

AmountAtMomentObserver - Class in fern.simulation.observer

Observes the amount of some molecule species at a certain moment.

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

Creates the observer for the given simulator, the given theta and the given species

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

Creates the observer for the given simulator, the given theta and the given species

AmountIntervalObserver - Class in fern.simulation.observer

Observes amounts of molecule species repeatedly after certain intervals.

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

Creates the observer for a given simulator, a given interval and given species indices

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

Creates the observer for a given simulator, a given interval and given species names.

AmountLowerThanController - Class in fern.simulation.controller

AmountLowerThanController(long, String) - Constructor for class fern.simulation.controller.AmountLowerThanController

AmountLowerThanController(long, int) - Constructor for class fern.simulation.controller.AmountLowerThanController

AmountManager - Interface in fern.network

The AmountManager is one of the most important connections between a Network and a Simulator.

AnalysisBase - Class in fern.analysis

This class can be used as a base class for many analysis algorithms (like AutocatalticNetworkDetection, ShortestPath, ...).

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

Creates an analysis instance.

AndController - Class in fern.simulation.controller

Implements a SimulationController composed of many SimulationController.

AndController(SimulationController...) - Constructor for class fern.simulation.controller.AndController

annotate(String, String) - Method in class fern.analysis.AutocatalyticNetworkDetection

Adds annotations to each autocatalytic reaction / species.

AnnotationManager - Interface in fern.network

AnnotationManager objects are the places, where static (or quasi-static) properties of a network are stored.

AnnotationManagerImpl - Class in fern.network

Base implementation of the AnnotationManager interface.

AnnotationManagerImpl() - Constructor for class fern.network.AnnotationManagerImpl

applyDefaultStyle(String) - Method in class fern.tools.gnuplot.Axes

Sets the style of each column to the default style except for columns that already have a style.

areEqual(Network, Network) - Static method in class fern.tools.NetworkTools

Gets whether or not the two given networks contain the same species, the same reactions and yield the same propensities when the amounts of each reactant are respectively 1, 5, 10, 100.

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

Gets the argmax of the given map.

ArrayKineticConstantPropensityCalculator - Class in fern.network

Implementation of an AbstractKineticConstantPropensityCalculator which uses an array to store the constants for each reaction.

ArrayKineticConstantPropensityCalculator(int[][], double[]) - Constructor for class fern.network.ArrayKineticConstantPropensityCalculator

Create the propensity calculator with given constants and given reactant adjacency arrays

ArrayMatrixAxes - Class in fern.tools.gnuplot

Implementation of Axes to use with array matrixes of any number type (the type of the arrays is inferred by using the reflection api).

ArrayMatrixAxes(Object) - Constructor for class fern.tools.gnuplot.ArrayMatrixAxes

Create a new Axes object containing the given array matrix without labels / styles.

ArrayMatrixAxes(Object, String[], String[]) - Constructor for class fern.tools.gnuplot.ArrayMatrixAxes

Create a new Axes object containing the given array matrix with the given labels /styles (either can be null).

AstNodeType - Variable in class fern.network.sbml.MathTree.InnerNode

AutocatalyticNetwork - Class in fern.network.creation

Evolve an autocatalytic network.

AutocatalyticNetwork(char[], Probability, Probability, int) - Constructor for class fern.network.creation.AutocatalyticNetwork

Creates the autocatalytic network from given monomers, reaction probability, catalysis probability up to a given polymer length.

AutocatalyticNetwork(char[], Probability, Probability, int, boolean) - Constructor for class fern.network.creation.AutocatalyticNetwork

Creates the autocatalytic network from given monomers, reaction probability, catalysis probability up to a given polymer length. useDefault should usually set to true unless you want to evolve really huge networks.

AutocatalyticNetworkDetection - Class in fern.analysis

Detects the autocatalytic set of the given network if there is any.

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

Creates the AutocatalyticDetection by using the in the network built in CatalystIterator.

AutocatalyticNetworkDetection(Network, CatalystIterator) - Constructor for class fern.analysis.AutocatalyticNetworkDetection

Creates the AutocatalyticDetection by using the second argument as CatalystIterator.

AutocatalyticNetworkExample - Class in fern.example

Here, the evolution of a reaction network as proposed by [1] is performed.

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

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

Gets the avg of the array

Axes - Class in fern.tools.gnuplot

Contains the data columns for GnuPlot.

Axes() - Constructor for class fern.tools.gnuplot.Axes