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

M

main(String[]) - Static method in class fern.benchmark.RandomNumber

main(String[]) - Static method in class fern.benchmark.SimulatorCorrectness

main(String[]) - Static method in class fern.cellDesigner.ui.MainFrame

main(String[]) - Static method in class fern.cytoscape.ui.MainFrame

main(String[]) - Static method in class fern.example.AutocatalyticNetworkExample

main(String[]) - Static method in class fern.example.CompositionRejectionStressTest

main(String[]) - Static method in class fern.example.DecayingDimerizingHistogramDistances

main(String[]) - Static method in class fern.example.DecayingDimerizingInteractive

main(String[]) - Static method in class fern.example.DecayingDimerizingPlots

Deprecated.

main(String[]) - Static method in class fern.example.Dsmts

main(String[]) - Static method in class fern.example.IrreversibleIsomerization

main(String[]) - Static method in class fern.example.LacYComplete

main(String[]) - Static method in class fern.example.LacYHistogramDistances

main(String[]) - Static method in class fern.example.LacZ

main(String[]) - Static method in class fern.example.Mapk

main(String[]) - Static method in class fern.example.MapkBenchmark

main(String[]) - Static method in class fern.example.MichaelisMentenKinetic

main(String[]) - Static method in class fern.example.SBMLMathTreeTest

Dumb the MathTrees of an SBML network to Stdout

main(String[]) - Static method in class fern.Start

MainFrame - Class in fern.cellDesigner.ui

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

MainFrame - Class in fern.cytoscape.ui

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

Mapk - Class in fern.example

The most basic example uses the famous enzyme kinetics equation by Michaelis and Menten S + E <-> ES -> P to introduce fundamental loading and repeated simulation of reaction networks.

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

MapkBenchmark - Class in fern.example

Use the signal transduction pathway network of the epidermal growth factor proposed by [1] to introduce the benchmark system.

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

MathTree - Class in fern.network.sbml

Representation of am evaluation tree.

MathTree(Network, ASTNode, Map<String, Double>, Map<String, Double>, Map<String, Integer>) - Constructor for class fern.network.sbml.MathTree

Creates a MathTree from an libsbml ASTNode.

MathTree.ConstLeaf - Class in fern.network.sbml

MathTree.ConstLeaf(double) - Constructor for class fern.network.sbml.MathTree.ConstLeaf

MathTree.GlobalLeaf - Class in fern.network.sbml

MathTree.GlobalLeaf(String) - Constructor for class fern.network.sbml.MathTree.GlobalLeaf

MathTree.InnerNode - Class in fern.network.sbml

MathTree.InnerNode(MathTree.Node[], int) - Constructor for class fern.network.sbml.MathTree.InnerNode

MathTree.Node - Class in fern.network.sbml

MathTree.Node() - Constructor for class fern.network.sbml.MathTree.Node

MathTree.VarLeaf - Class in fern.network.sbml

MathTree.VarLeaf(String, int) - Constructor for class fern.network.sbml.MathTree.VarLeaf

max(Iterable<Integer>) - Static method in class fern.tools.NumberTools

Gets the maximal value within the given Iterable.

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

Merges another gnuplot object with this one by add its axes and copy its default style to the axes (if they have no style).

MichaelisMentenKinetic - Class in fern.example

The most basic example uses the famous enzyme kinetics equation by Michaelis and Menten S + E <-> ES -> P to introduce fundamental loading and repeated simulation of reaction networks.

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

min(Iterable<Integer>) - Static method in class fern.tools.NumberTools

Gets the minimal value within the given Iterable.

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

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

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

ModifierNetwork - Class in fern.network.modification

Base class for modified networks, which implements the full Network interface.

ModifierNetwork(Network) - Constructor for class fern.network.modification.ModifierNetwork

Creates a ModifierNetwork from an original network.

MultiAmountIntervalObserver - Class in fern.simulation.observer

Observes amounts of molecule species repeatedly after certain intervals.

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

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

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

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

MultiplierNetwork - Class in fern.network.modification

Multiplies the whole network by a factor.

MultiplierNetwork(Network, int) - Constructor for class fern.network.modification.MultiplierNetwork

Creates a new network from an original network and virtually multiplies each reaction and species factor times.