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

D

DecayingDimerizingHistogramDistances - Class in fern.example

Demonstration of performance and accuracy differences of the different simulation algorithms.

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

DecayingDimerizingInteractive - Class in fern.example

Demonstration of performance and accuracy differences of the different simulation algorithms.

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

DecayingDimerizingPlots - Class in fern.example

Deprecated.

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

Deprecated.

DefaultAmountManager - Class in fern.network

Default implementation of an amount manager, that stores the amounts in arrays.

DefaultAmountManager(Network) - Constructor for class fern.network.DefaultAmountManager

Creates an AmountManager for a given network

DefaultController - Class in fern.simulation.controller

The probably most common implementation of an SimulationController.

DefaultController(double) - Constructor for class fern.simulation.controller.DefaultController

Creates the controller for a given time where the simulation has to stop.

DependencyGraph - Class in fern.simulation.algorithm

Implements a dependency graph.

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

Creates the dependency graph for a given network

describe() - Method in class fern.cytoscape.CytoscapeVisualizer

detect() - Method in class fern.analysis.AutocatalyticNetworkDetection

Performs the detection algorithm.

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

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

drawReaction(Stochastics, double[]) - Method in class fern.simulation.algorithm.GroupContainer

Dsmts - Class in fern.example

Perform a series of tests (refer to http://www.calibayes.ncl.ac.uk/Resources/dsmts).

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

dumpMathTree(MathTree) - Static method in class fern.tools.NetworkTools

Dumps the MathTree to stdout.

dumpMathTree(MathTree, Writer) - Static method in class fern.tools.NetworkTools

Dumps the math tree to the given Writer.

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

Dumps the network to stdout.

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

Dumps the network to the given Writer.