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

F

faculty(int) - Static method in class fern.tools.NumberTools

Gets the faculty

FeatureNotSupportedException - Exception in fern.network

FeatureNotSupportedException(String) - Constructor for exception fern.network.FeatureNotSupportedException

fern - package fern

fern.analysis - package fern.analysis

Provides classes and algorithms for analysing networks like ShortestPath, AutocatalyticDetection.

fern.benchmark - package fern.benchmark

Provides classes for benchmarking simulations (time benchmarks, histogram distance calculation).

fern.cellDesigner - package fern.cellDesigner

fern.cellDesigner.ui - package fern.cellDesigner.ui

fern.cytoscape - package fern.cytoscape

Provides the classes for the cytoscape plugin.

fern.cytoscape.ui - package fern.cytoscape.ui

fern.example - package fern.example

Contains examples and demonstrations of the framework.

fern.network - package fern.network

Provides general classes and interfaces for storing network data.

fern.network.creation - package fern.network.creation

Provides classes for the evolution of networks.

fern.network.fernml - package fern.network.fernml

Provides the classes for parsing and using FernML based networks.

fern.network.modification - package fern.network.modification

Provides classes for modifications of networks.

fern.network.sbml - package fern.network.sbml

Provides the classes for parsing and using sbml based networks.

fern.simulation - package fern.simulation

Provides algorithms for simulating reaction network as well as methods for observer certain aspects of a simulation.

fern.simulation.algorithm - package fern.simulation.algorithm

Provides algorithms for stochastic simultion of reaction networks.

fern.simulation.controller - package fern.simulation.controller

Provides classes to control the simulations.

fern.simulation.observer - package fern.simulation.observer

Provides classes to observe certain aspects of simulations.

fern.tools - package fern.tools

Provides common used tools.

fern.tools.functions - package fern.tools.functions

Provides common function delegates and implementations.

fern.tools.gnuplot - package fern.tools.gnuplot

Provides classes to use gnuplot from java.

FernCellDesignerPlugin - Class in fern.cellDesigner

FernCellDesignerPlugin() - Constructor for class fern.cellDesigner.FernCellDesignerPlugin

FernMLAnnotationManager - Class in fern.network.fernml

AnnotationManager for FernMLNetworks.

FernMLAnnotationManager(Element) - Constructor for class fern.network.fernml.FernMLAnnotationManager

Create the AnnotationManager from the root element of the jdom tree.

FernMLNetwork - Class in fern.network.fernml

A FernMLNetwork is usually loaded from a file.

FernMLNetwork(File) - Constructor for class fern.network.fernml.FernMLNetwork

Creates a FernMLNetwork from a file.

FernMLNetwork(Network) - Constructor for class fern.network.fernml.FernMLNetwork

Create a FernMLNetwork from an existing Network.

FernMLNetwork(Network, double[]) - Constructor for class fern.network.fernml.FernMLNetwork

Creates a FernMLNetwork out of an existing network (e.g. to save it to a fernml file) using explicitly given kineticConstants (when net doesn't use KineticConstantPropensityCalculator If kineticConstants is null or to short, a default value of 1 is taken.

FernVisualStyle - Class in fern.cytoscape

FernVisualStyle() - Constructor for class fern.cytoscape.FernVisualStyle

find(String) - Static method in class fern.example.ExamplePath

finished() - Method in interface fern.analysis.NetworkSearchAction

Gets called, when the search is done.

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

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

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

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

Do nothing.

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

Calculates the average over all runs of the simulator.

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

Prints event.

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

Adds the recorded data to the average data pool.

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

Do nothing.

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

Gets called when a simulation has finished, directly after the termination check.

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

Calculates the average.

FireTypeObserver - Class in fern.simulation.observer

Observes the different types of firings.

FireTypeObserver(Simulator) - Constructor for class fern.simulation.observer.FireTypeObserver

Create the observer for the given simulator.