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

T

TauLeapingAbsoluteBoundSimulator - 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.

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

TauLeapingRelativeBoundSimulator - 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.

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

TauLeapingSpeciesPopulationBoundSimulator - 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.

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

theta(double) - Method in class fern.cytoscape.CytoscapeColorChangeObserver

theta(double) - Method in class fern.example.CellGrowthObserver

theta(double) - Method in class fern.network.sbml.SBMLEventHandlerObserver

theta(double) - Method in class fern.simulation.observer.AmountAtMomentObserver

Records the amounts of the species and puts it into the histogram.

theta(double) - Method in class fern.simulation.observer.FireTypeObserver

Do nothing.

theta(double) - Method in class fern.simulation.observer.InstantOutputObserver

Prints event.

theta(double) - Method in class fern.simulation.observer.IntervalObserver

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

theta(double) - Method in class fern.simulation.observer.LeapObserver

Do nothing.

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

Gets called by simulators when a certain moment in time is reached.

theta(double) - Method in class fern.simulation.observer.RandomNumberGeneratorCallObserver

Do nothing.

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

toArray(Collection<Integer>) - Static method in class fern.tools.NumberTools

Copies the values of the given collection and unboxes them to an array.

toArray(Collection<Double>) - Static method in class fern.tools.NumberTools

Copies the values of the given collection and unboxes them to an array.

toGnuplot(String[], String[]) - Method in class fern.benchmark.Benchmark

Adds the benchmark data without conversion to a new GnuPlot object.

toGnuplot(GnuPlot, String[], String[]) - Method in class fern.benchmark.Benchmark

Adds the benchmark data without conversion to a given GnuPlot object.

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

toGnuplot(GnuPlot) - Method in class fern.simulation.observer.AmountAtMomentObserver

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

toGnuplot(GnuPlot) - Method in class fern.simulation.observer.FireTypeObserver

toGnuplot() - Method in interface fern.simulation.observer.GnuPlotObserver

Creates a new GnuPlot object and passes the actual observer data to it.

toGnuplot(GnuPlot) - Method in interface fern.simulation.observer.GnuPlotObserver

Passes the actual observer data to a GnuPlot object.

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

toGnuplot(GnuPlot) - Method in class fern.simulation.observer.IntervalObserver

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

toGnuplot(GnuPlot) - Method in class fern.simulation.observer.LeapObserver

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

toGnuplot(GnuPlot) - Method in class fern.simulation.observer.RandomNumberGeneratorCallObserver

toGnuPlotAsHistogram(String[], String[]) - Method in class fern.benchmark.Benchmark

Adds the benchmark data as histogram to a new GnuPlot object.

toGnuPlotAsHistogram(GnuPlot, String[], String[]) - Method in class fern.benchmark.Benchmark

Adds the benchmark data as histogram to a given GnuPlot object.

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

Creates a new GnuPlot object and passes the recent observer data to it.

toGnuplotRecent(GnuPlot) - Method in class fern.simulation.observer.IntervalObserver

Passes the recent observer data to a GnuPlot object.

toString() - Method in class fern.analysis.ShortestPath.Path

toString() - Method in class fern.network.sbml.MathTree.ConstLeaf

toString() - Method in class fern.network.sbml.MathTree.GlobalLeaf

toString() - Method in class fern.network.sbml.MathTree.InnerNode

toString() - Method in class fern.network.sbml.MathTree.VarLeaf

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

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

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

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

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

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

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

TransposedArrayMatrixAxes - Class in fern.tools.gnuplot

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

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

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

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

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

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

trigger() - Method in class fern.simulation.observer.TriggerObserver

Is executed, whenever a event can trigger (before step and during a theta event).

TriggerObserver - Class in fern.simulation.observer

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

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