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

G

get() - Method in class fern.analysis.IntQueue

get() - Method in interface fern.analysis.IntSearchStructure

get() - Method in class fern.analysis.IntStack

getA_sum() - Method in class fern.simulation.algorithm.GroupContainer

getAdditionalReactionNeighbors(int) - Method in interface fern.analysis.NetworkSearchAction

Returns an iterator for additional neighbors of this species

getAdditionalSpeciesNeighbors(int) - Method in interface fern.analysis.NetworkSearchAction

Returns an iterator for additional neighbors of this reaction

getAmount(int) - Method in interface fern.network.AmountManager

Gets the current amount of a species.

getAmount(int) - Method in class fern.network.ConstantAmountManager

getAmount(int) - Method in class fern.network.DefaultAmountManager

Gets the current amount of a species.

getAmount(int) - Method in class fern.simulation.Simulator

Gets the amount of the given species.

getAmountBottomColor() - Method in class fern.cytoscape.ColorCalculator

getAmountManager() - Method in class fern.network.AbstractNetworkImpl

getAmountManager() - Method in class fern.network.modification.CatalysedNetwork

getAmountManager() - Method in class fern.network.modification.ExtractSubNetwork

Gets the AmountManager for the extracted subnet.

getAmountManager() - Method in class fern.network.modification.ModifierNetwork

Gets the AmountManager of the original network.

getAmountManager() - Method in class fern.network.modification.MultiplierNetwork

Gets the AmountManager for the modified network.

getAmountManager() - Method in class fern.network.modification.ReversibleNetwork

Gets the AmountManager for the modified network.

getAmountManager() - Method in interface fern.network.Network

Gets the AmountManager for this network.

getAmountTopColor() - Method in class fern.cytoscape.ColorCalculator

getAnnotationManager() - Method in class fern.network.AbstractNetworkImpl

getAnnotationManager() - Method in class fern.network.modification.CatalysedNetwork

getAnnotationManager() - Method in class fern.network.modification.ExtractSubNetwork

Gets an AnnotationManager for the redirected index space.

getAnnotationManager() - Method in class fern.network.modification.ModifierNetwork

Gets the AnnotationManager of the original network

getAnnotationManager() - Method in class fern.network.modification.MultiplierNetwork

Gets the AnnotationManager for the modified network.

getAnnotationManager() - Method in class fern.network.modification.ReversibleNetwork

Gets the AnnotationManager for the modified network.

getAnnotationManager() - Method in interface fern.network.Network

Gets the AnnotationManager for this network.

getAsDouble(String) - Method in class fern.tools.ConfigReader

Gets the value of the line key=value as double

getAsInt(String) - Method in class fern.tools.ConfigReader

Gets the value of the line key=value as int

getAsString(String) - Method in class fern.tools.ConfigReader

Gets the value of the line key=value as string

getAsStringArr(String) - Method in class fern.tools.ConfigReader

Gets the value of the line key=value as string array (the value is simply splitted by ,)

getAttributeKeys() - Method in class fern.cytoscape.ui.ExtendedPane

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

Gets the autocatalytic reactions as BitVector.

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

Gets the autocatalytic species as BitVector.

getAvailableTypes() - Static method in class fern.network.NetworkLoader

Gets types of networks that are readable by FERN.

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

Returns the Axes object containing the data, labels and styles.

getBinom(int, double) - Method in class fern.tools.Stochastics

Gets a random number from the binomial distribution.

getCatalysts(int) - Method in class fern.network.creation.AutocatalyticNetwork

Implementation for the CatalystIterator.

getCatalysts(int) - Method in interface fern.network.creation.CatalystIterator

Gets the indices of the catalysts of a reaction.

getCatalyzedKineticConstant() - Method in class fern.network.creation.AutocatalyticNetwork

Gets the kinetic constant for catalyzed reactions.

getColor(double, double) - Method in class fern.cytoscape.ColorCalculator

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

Returns the list of commands, e.g. if you want to remove some command from it.

getConstant(int) - Method in class fern.network.ArrayKineticConstantPropensityCalculator

getConstant(int) - Method in interface fern.network.KineticConstantPropensityCalculator

Gets the constant for a reaction

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

Gets the reaction rate constant by setting the reactant amounts to the stoichiometric coefficient.

getConstantFromDeterministicRateConstant(double, int, double) - Method in class fern.network.AbstractKineticConstantPropensityCalculator

Calculates the specific reaction probability rate constant c from the conventional deterministic rate constant k in some fixed volume v by the formula c=|reactants| !

getConstantFromDeterministicRateConstant(double, int, double) - Method in interface fern.network.KineticConstantPropensityCalculator

Calculates the specific reaction probability rate constant c from the conventional deterministic rate constant k in some fixed volume v by the formula c=|reactants| !

getContentAsArray(BitVector) - Static method in class fern.tools.NumberTools

Gets the indices of the set bits of the given BitVector as array.

getContentAsBitVector(int[]) - Static method in class fern.tools.NumberTools

Gets the content of the given array as BitVector, which means, that the BitVector will have a size equal to the maximal value in the array and contains a 1 for each element which is contained at least once in the array

getCounts() - Method in class fern.tools.Stochastics

Gets the number of random number generations for each distribution (same order as in Stochastics.getNames() since the last call of resetCounts.

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

Returns the data in gnuplot data file format as list containing the data for each added axes.

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

The defaultStyle is used, when no style is defined for an column in an axes object.

getDependent(int) - Method in class fern.simulation.algorithm.DependencyGraph

Gets the descendants of a reaction in the dependency graph

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

Gets if this Axes object contains 2 or 3 dimensional data.

getEdgeClassifier() - Method in class fern.cytoscape.NetworkChecker

getEpsilon() - Method in class fern.cellDesigner.ui.ExtendedPane

getEpsilon() - Method in class fern.cytoscape.ui.ExtendedPane

getEpsilon() - Method in class fern.example.HistogramDistanceTestSet

getEpsilon() - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

The epsilon is an error control parameter and bounds the expected change of the propensity functions by epsilon * a_sum.

getExponential(double) - Method in class fern.tools.Stochastics

Gets a random number from the exponential distribution.

getFile() - Method in class fern.example.HistogramDistanceTestSet

getFinalValue(int) - Method in class fern.simulation.observer.IntervalObserver

Gets the last value of the given entity.

getGlobalParameters() - Method in class fern.cellDesigner.CellDesignerPropensityCalculator

Gets the global parameters.

getGlobalParameters() - Method in class fern.network.sbml.SBMLPropensityCalculator

Gets the global parameters.

getGrayScaleSpectrum(float) - Static method in class fern.tools.ColorSpectrum

Gets a gray scale color representing the given number, 0 means white, 1 means black.

getHistoAsParallelArray() - Method in class fern.example.HistogramDistanceTestSet

getHistogram() - Method in class fern.example.HistogramDistanceTestSet

getHistogram(int) - Method in class fern.simulation.observer.AmountAtMomentObserver

Gets the histogram of the distribution for a species

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

Gets a string representation of the histogram map.

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

Return the plotted data as image.

getInitialAmount(int) - Method in class fern.cellDesigner.CellDesignerNetworkWrapper

getInitialAmount(int) - Method in class fern.cytoscape.CytoscapeNetworkWrapper

getInitialAmount(int) - Method in class fern.network.creation.AutocatalyticNetwork

getInitialAmount(int) - Method in class fern.network.fernml.FernMLNetwork

getInitialAmount(int) - Method in class fern.network.modification.ExtractSubNetwork

getInitialAmount(int) - Method in class fern.network.modification.ModifierNetwork

getInitialAmount(int) - Method in interface fern.network.Network

Gets the initial amount of the specified molecule species.

getInitialAmount(int) - Method in class fern.network.sbml.SBMLNetwork

getInstance() - Static method in class fern.tools.Stochastics

Singleton pattern method.

getKey(int) - Method in class fern.simulation.algorithm.IndexedPriorityQueue

Gets the tau of a reaction by lookup in the index

getKineticLawSpecies(int) - Method in class fern.cellDesigner.CellDesignerPropensityCalculator

getKineticLawSpecies(int) - Method in interface fern.network.ComplexDependenciesPropensityCalculator

Gets the indices of the species that are included in the calculation of the given reaction.

getKineticLawSpecies(int) - Method in class fern.network.sbml.SBMLPropensityCalculator

getLabel(int) - Method in class fern.tools.gnuplot.Axes

Gets the label for a column.

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

Gets the label format of Observer.getLabel(String).

getLangevinThreshold() - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

The Langevin threshold determines, when the normal distribution is used as an approximation for the poisson distribution.

getMathTree(int) - Method in class fern.network.sbml.SBMLPropensityCalculator

Gets the internal representation of the sbml kinetic law.

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

Gets the index of the minimal tau in the queue.

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

Gets the minimal tau in the queue.

getMonomerAmount() - Method in class fern.network.creation.AutocatalyticNetwork

Gets the initial amount of the monomers for a simulation algorithm.

getName() - Method in class fern.network.AbstractNetworkImpl

getName() - Method in class fern.network.modification.ModifierNetwork

Gets the name of the original network

getName() - Method in interface fern.network.Network

Gets an identifier of the network.

getName() - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

Returns the name of this simulator

getName() - Method in class fern.simulation.algorithm.CompositionRejection

getName() - Method in class fern.simulation.algorithm.GibsonBruckSimulator

getName() - Method in class fern.simulation.algorithm.GillespieEnhanced

getName() - Method in class fern.simulation.algorithm.GillespieSimple

getName() - Method in class fern.simulation.algorithm.HybridMaximalTimeStep

getName() - Method in class fern.simulation.algorithm.TauLeapingAbsoluteBoundSimulator

getName() - Method in class fern.simulation.algorithm.TauLeapingRelativeBoundSimulator

getName() - Method in class fern.simulation.algorithm.TauLeapingSpeciesPopulationBoundSimulator

getName() - Method in class fern.simulation.Simulator

Gets the name of the algorithm.

getNames() - Method in class fern.tools.Stochastics

Gets the names of the built-in distributions.

getNc() - Method in class fern.cellDesigner.ui.ExtendedPane

getNc() - Method in class fern.cytoscape.ui.ExtendedPane

getNCritical() - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

The nCritical determines, when a reaction is called critical.

getNet() - Method in class fern.simulation.Simulator

Gets the simulation network.

getNetwork() - Method in class fern.cellDesigner.ui.MainFrame

getNetwork() - Method in class fern.cytoscape.ui.MainFrame

getNetworkAnnotation(String) - Method in class fern.cytoscape.CytoscapeAnnotationManager

getNetworkAnnotation(String) - Method in interface fern.network.AnnotationManager

Gets the network annotation of the specified field.

getNetworkAnnotation(String) - Method in class fern.network.AnnotationManagerImpl

getNetworkAnnotation(String) - Method in class fern.network.fernml.FernMLAnnotationManager

getNetworkAnnotationTypes() - Method in class fern.cytoscape.CytoscapeAnnotationManager

getNetworkAnnotationTypes() - Method in interface fern.network.AnnotationManager

Gets the names of the network reaction.

getNetworkAnnotationTypes() - Method in class fern.network.AnnotationManagerImpl

getNetworkAnnotationTypes() - Method in class fern.network.fernml.FernMLAnnotationManager

getNetworkChecker() - Method in class fern.cytoscape.CytoscapeNetworkWrapper

getNetworkChecker() - Method in class fern.cytoscape.ui.MainFrame

getNetworkViewObject() - Method in class fern.cytoscape.CytoscapeNetworkWrapper

getNextThetaEvent() - Method in class fern.simulation.Simulator

Theta defines a moment, where the simulator has to invoke theta of a observer.

getNodeAttributeObject() - Method in class fern.cytoscape.CytoscapeNetworkWrapper

getNodeClassifier() - Method in class fern.cytoscape.NetworkChecker

getNodeParameter() - Method in class fern.cytoscape.NetworkChecker

getNormal() - Method in class fern.tools.Stochastics

Gets a random number from the Normal distribution

getNormal(double, double) - Method in class fern.tools.Stochastics

Gets a random number from the Normal distribution with given mean and stddev.

getNum() - Method in class fern.cellDesigner.ui.ExtendedPane

getNum() - Method in class fern.cytoscape.ui.ExtendedPane

getNumber(int, int) - Method in class fern.tools.gnuplot.Axes

Gets the entry of this axes at the specified position.

getNumber(int, int) - Method in class fern.tools.gnuplot.TransposedArrayMatrixAxes

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

Gets the numbers from 0 to n in an array.

getNumBins() - Method in class fern.benchmark.Benchmark

Gets the number of bins that are used for creating gnuplot histograms.

getNumColumns() - Method in class fern.tools.gnuplot.ArrayMatrixAxes

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

Gets the number of columns.

getNumColumns() - Method in class fern.tools.gnuplot.CollectionAxes

getNumColumns() - Method in class fern.tools.gnuplot.TransposedArrayMatrixAxes

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

Gets the number of the performed leaps

getNumMonomers() - Method in class fern.network.creation.AutocatalyticNetwork

Gets if the number of monomers

getNumReactions() - Method in class fern.network.AbstractNetworkImpl

getNumReactions() - Method in class fern.network.fernml.FernMLNetwork

getNumReactions() - Method in class fern.network.modification.CatalysedNetwork

getNumReactions() - Method in class fern.network.modification.ExtractSubNetwork

Gets the number of reactions in the extracted subnet.

getNumReactions() - Method in class fern.network.modification.ModifierNetwork

Gets the number of reaction in the original network.

getNumReactions() - Method in class fern.network.modification.MultiplierNetwork

Gets the number of reactions in the modified network (which is 2*number of reaction in the original network).

getNumReactions() - Method in class fern.network.modification.ReversibleNetwork

Gets the number of reactions in the modified network (which is 2*number of reaction in the original network).

getNumReactions() - Method in interface fern.network.Network

Gets the number of reaction within the network.

getNumRows() - Method in class fern.tools.gnuplot.ArrayMatrixAxes

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

Gets the number of rows.

getNumRows() - Method in class fern.tools.gnuplot.CollectionAxes

getNumRows() - Method in class fern.tools.gnuplot.TransposedArrayMatrixAxes

getNumRuns() - Method in class fern.cellDesigner.ui.OverviewPane

getNumRuns() - Method in class fern.cytoscape.ui.OverviewPane

getNumSimpleCalls() - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

The numSimpleCalls determines, how often the SSA is called, when tau leaping is abandoned.

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

Gets the number of finished repeats of the simulation.

getNumSpecies() - Method in class fern.network.AbstractNetworkImpl

getNumSpecies() - Method in class fern.network.fernml.FernMLNetwork

getNumSpecies() - Method in class fern.network.modification.ExtractSubNetwork

Gets the number of species in the extracted subnet.

getNumSpecies() - Method in class fern.network.modification.ModifierNetwork

Gets the number of species in the original network.

getNumSpecies() - Method in interface fern.network.Network

Gets the number of species within the network.

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

Gets the number of steps taken in one simulation

getOriginalNetwork() - Method in class fern.network.modification.ModifierNetwork

Gets the original network.

getOtherAmount() - Method in class fern.network.creation.AutocatalyticNetwork

Gets the initial amount of the not-monomers for a simulation algorithm.

getParentNetwork() - Method in class fern.network.modification.ModifierNetwork

Gets the parent network.

getPlotCommand(List<File>) - Method in class fern.tools.gnuplot.GnuPlot

Returns the plot command for a given filename

getPoisson(double) - Method in class fern.tools.Stochastics

Gets a random number from the Poisson distribution.

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

Gets the registered PrintWriter

getProb(int, int) - Method in class fern.tools.functions.Probability.Constant

getProb(int, int) - Method in interface fern.tools.functions.Probability

Gets the probability depending on two integers.

getProb(int, int) - Method in class fern.tools.functions.Probability.ReactionProbability

getProducts(int) - Method in class fern.network.AbstractNetworkImpl

getProducts(int) - Method in class fern.network.modification.CatalysedNetwork

getProducts(int) - Method in class fern.network.modification.ExtractSubNetwork

Gets the products of a reaction.

getProducts(int) - Method in class fern.network.modification.ModifierNetwork

Gets the products of a reaction in the original network.

getProducts(int) - Method in class fern.network.modification.MultiplierNetwork

Gets the products of a reaction

getProducts(int) - Method in class fern.network.modification.ReversibleNetwork

Gets the products of a reaction

getProducts(int) - Method in interface fern.network.Network

Gets the products of the specified reaction.

getPropensity(int) - Method in class fern.simulation.Simulator

Gets the current propensity for the given reaction.

getPropensityCalculator() - Method in class fern.network.AbstractNetworkImpl

getPropensityCalculator() - Method in class fern.network.fernml.FernMLNetwork

getPropensityCalculator() - Method in class fern.network.modification.CatalysedNetwork

getPropensityCalculator() - Method in class fern.network.modification.ExtractSubNetwork

Gets the PropensityCalculator for the extracted subnet.

getPropensityCalculator() - Method in class fern.network.modification.ModifierNetwork

Gets the PropensityCalculator of the original network.

getPropensityCalculator() - Method in class fern.network.modification.MultiplierNetwork

Gets the PropensityCalculator for the modified network.

getPropensityCalculator() - Method in class fern.network.modification.ReversibleNetwork

Gets the PropensityCalculator for the modified network.

getPropensityCalculator() - Method in interface fern.network.Network

Gets the PropensityCalculator for this network.

getPropensityCalculator() - Method in class fern.simulation.Simulator

Gets the PropensityCalculator.

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

Returns the raw path: Is ends with a species index and is composed of alternating indices of species and reactions.

getReactants(int) - Method in class fern.network.AbstractNetworkImpl

getReactants(int) - Method in class fern.network.modification.CatalysedNetwork

getReactants(int) - Method in class fern.network.modification.ExtractSubNetwork

Gets the reactants of a reaction.

getReactants(int) - Method in class fern.network.modification.ModifierNetwork

Gets the reactants of a reaction in the original network.

getReactants(int) - Method in class fern.network.modification.MultiplierNetwork

Gets the reactants of a reaction

getReactants(int) - Method in class fern.network.modification.ReversibleNetwork

Gets the reactants of a reaction

getReactants(int) - Method in interface fern.network.Network

Gets the reactants of the specified reaction.

getReactionAnnotation(int, String) - Method in class fern.cytoscape.CytoscapeAnnotationManager

getReactionAnnotation(int, String) - Method in interface fern.network.AnnotationManager

Gets the reaction annotation of the specified field.

getReactionAnnotation(int, String) - Method in class fern.network.AnnotationManagerImpl

getReactionAnnotation(int, String) - Method in class fern.network.fernml.FernMLAnnotationManager

getReactionAnnotationTypes(int) - Method in class fern.cytoscape.CytoscapeAnnotationManager

getReactionAnnotationTypes(int) - Method in interface fern.network.AnnotationManager

Gets the names of the species reaction.

getReactionAnnotationTypes(int) - Method in class fern.network.AnnotationManagerImpl

getReactionAnnotationTypes(int) - Method in class fern.network.fernml.FernMLAnnotationManager

getReactionCoefficient(Node) - Method in class fern.cytoscape.NetworkChecker.NodeParameter

getReactionColor() - Method in class fern.cytoscape.ColorCalculator

getReactionName(int) - Method in class fern.network.AbstractNetworkImpl

getReactionName(int) - Method in class fern.network.modification.CatalysedNetwork

getReactionName(int) - Method in class fern.network.modification.ExtractSubNetwork

Gets a string representation of the reaction

getReactionName(int) - Method in class fern.network.modification.ModifierNetwork

Gets a string representation of the reactio in the original network.

getReactionName(int) - Method in class fern.network.modification.MultiplierNetwork

Gets a string representation of the reaction in the modified network.

getReactionName(int) - Method in class fern.network.modification.ReversibleNetwork

Gets a string representation of the reaction in the modified network.

getReactionName(int) - Method in interface fern.network.Network

Gets a string representation of the reaction.

getReactionNames(Network, int[]) - Static method in class fern.tools.NetworkTools

Transforms the reaction indices in the given array to the corresponding names.

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

Gets a string representation of the given reactions and the amounts of each participating species in parentheses.

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

Returns all the reactions on this path.

getReactionsOf(Network, String[]) - Static method in class fern.tools.NetworkTools

Gets the reaction whose products / reactants are in speciesName

getReactionView(int) - Method in class fern.cytoscape.CytoscapeNetworkWrapper

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

Gets the recorded data of the most recent simulation run.

getRecordStart() - Method in class fern.simulation.observer.ReactionIntervalObserver

Gets the moment in time where the recording starts

getReversePropensityCalculator() - Method in class fern.network.creation.AutocatalyticNetwork

Gets the PropensityCalculator which has to be used for instantiation of the ReversibleNetwork.

getRoot() - Method in class fern.network.sbml.MathTree

Gets the root of this MathTree.

getSBMLModel() - Method in class fern.network.sbml.SBMLNetwork

Gets the libsbml model.

getScale() - Method in class fern.cytoscape.ColorCalculator

getScaleMax() - Method in class fern.cytoscape.ColorCalculator

getSeed() - Method in class fern.tools.Stochastics

Gets the actual seed of the random number generator.

getShowSteps() - Method in class fern.benchmark.SimulatorPerformance

Gets the number of iterations between two present-calls.

getSimulator() - Method in class fern.cellDesigner.ui.OverviewPane

getSimulator() - Method in class fern.cytoscape.ui.OverviewPane

getSimulator() - Method in class fern.example.HistogramDistanceTestSet

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

Gets the simulator

getSimulators() - Method in class fern.benchmark.SimulatorPerformance

Gets the simulators used by this benchmark.

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

Returns all the species on this path.

getSpecies() - Method in class fern.network.sbml.MathTree

Gets the species present in this tree.

getSpeciesAnnotation(int, String) - Method in class fern.cytoscape.CytoscapeAnnotationManager

getSpeciesAnnotation(int, String) - Method in interface fern.network.AnnotationManager

Gets the species annotation of the specified field.

getSpeciesAnnotation(int, String) - Method in class fern.network.AnnotationManagerImpl

getSpeciesAnnotation(int, String) - Method in class fern.network.fernml.FernMLAnnotationManager

getSpeciesAnnotationTypes(int) - Method in class fern.cytoscape.CytoscapeAnnotationManager

getSpeciesAnnotationTypes(int) - Method in interface fern.network.AnnotationManager

Gets the names of the species annotations.

getSpeciesAnnotationTypes(int) - Method in class fern.network.AnnotationManagerImpl

getSpeciesAnnotationTypes(int) - Method in class fern.network.fernml.FernMLAnnotationManager

getSpeciesByName(String) - Method in class fern.network.AbstractNetworkImpl

getSpeciesByName(String) - Method in class fern.network.modification.ExtractSubNetwork

Gets the index of the species by its name.

getSpeciesByName(String) - Method in class fern.network.modification.ModifierNetwork

Gets the index of the species by its name in the original network.

getSpeciesByName(String) - Method in interface fern.network.Network

Gets the species index by name.

getSpeciesIndices(Network, String[]) - Static method in class fern.tools.NetworkTools

Transforms the species names in the given array to the corresponding indices.

getSpeciesInitialAmount(Node) - Method in class fern.cytoscape.NetworkChecker.NodeParameter

getSpeciesMapping() - Method in class fern.network.AbstractNetworkImpl

Gets the mapping from species names to their indices.

getSpeciesName(int) - Method in class fern.network.AbstractNetworkImpl

getSpeciesName(int) - Method in class fern.network.modification.ExtractSubNetwork

Gets the name of the species with given index.

getSpeciesName(int) - Method in class fern.network.modification.ModifierNetwork

Gets the name of the species by index in the original network.

getSpeciesName(int) - Method in interface fern.network.Network

Gets the species name by index.

getSpeciesNames(Network, int[]) - Static method in class fern.tools.NetworkTools

Transforms the species indices in the given array to the corresponding names.

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

Gets the species names together with its actual amount in parentheses

getSpeciesView(int) - Method in class fern.cytoscape.CytoscapeNetworkWrapper

getSpectrum(float, Color...) - Static method in class fern.tools.ColorSpectrum

Gets a color representing the given number in an given color scale.

getStyle(int) - Method in class fern.tools.gnuplot.Axes

Gets the style for a column.

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

getStyles() - Method in class fern.simulation.observer.AmountIntervalObserver

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

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

Gets the styles for the columns.

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

getStyles() - Method in class fern.simulation.observer.MultiAmountIntervalObserver

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

getStyles() - Method in class fern.simulation.observer.ReactionIntervalObserver

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

Gets the moment in time, where the simulator has to invoke Observer.theta(double).

getThreshold() - Method in class fern.cellDesigner.ui.ExtendedPane

getThreshold() - Method in class fern.cytoscape.ui.ExtendedPane

getTime() - Method in class fern.cellDesigner.ui.OverviewPane

getTime() - Method in class fern.cytoscape.ui.OverviewPane

getTime() - Method in class fern.simulation.controller.DefaultController

Gets the time where the simulation has to stop.

getTime() - Method in class fern.simulation.Simulator

Gets the actual simulation time.

getTrendSpecies() - Method in class fern.cellDesigner.ui.ExtendedPane

getTrendSpecies() - Method in class fern.cytoscape.ui.ExtendedPane

getUncatalyzedKineticConstant() - Method in class fern.network.creation.AutocatalyticNetwork

Gets the kinetic constant for not catalyzed reactions.

getUnif() - Method in class fern.tools.Stochastics

Gets a random number from the uniform distribution between 0 and 1.

getUnif(int, int) - Method in class fern.tools.Stochastics

Gets a uniformly chosen random number between min (inclusive) and max (exclusive)

getUseSimpleFactor() - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping

The useSimpleFactor determines, when the tau leaping is abandoned and the SSA method is used (if taugetVolume() - Method in class fern.simulation.Simulator

Gets the volume of the reaction network.

getX(int) - Method in class fern.tools.gnuplot.Axes

GibsonBruckSimulator - Class in fern.simulation.algorithm

Implementation of the algorithm of Gibson and Bruck.

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

GillespieEnhanced - Class in fern.simulation.algorithm

This is an enhanced version of the original Direct method developed by Gillespie.

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

GillespieSimple - Class in fern.simulation.algorithm

Implementation of Gillespie's Direct method.

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

GnuPlot - Class in fern.tools.gnuplot

The class GnuPlot provides methods for handling gnuplot data.

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

The constructor sets the DefaultCloseOperation of this JFrame to DISPOSE_ON_CLOSE.

GnuPlotObserver - Interface in fern.simulation.observer

Interface for certain observer which can produce gnuplot data.

goOn(Simulator) - Method in class fern.simulation.controller.AmountLowerThanController

goOn(Simulator) - Method in class fern.simulation.controller.AndController

goOn(Simulator) - Method in class fern.simulation.controller.DefaultController

goOn(Simulator) - Method in class fern.simulation.controller.OrController

goOn(Simulator) - Method in interface fern.simulation.controller.SimulationController

Returns whether or not to go on with the given simulation

goOn(Simulator) - Method in class fern.simulation.observer.AmountAtMomentObserver

Causes the simulator to stop when theta has been passed and the amounts have been recorded.

GroupContainer - Class in fern.simulation.algorithm

GroupContainer(Simulator) - Constructor for class fern.simulation.algorithm.GroupContainer