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

I

Index - Variable in class fern.network.sbml.MathTree.VarLeaf

IndexedPriorityQueue - Class in fern.simulation.algorithm

Implements an indexed priority queue.

IndexedPriorityQueue(double[]) - Constructor for class fern.simulation.algorithm.IndexedPriorityQueue

Creates a IndexedPriorityQueue from the given taus

inferStringFromSBMLConstant(String, Object) - Static method in class fern.network.sbml.MathTree

Uses reflection to get a string representation of a libsml constant.

initialAmount - Variable in class fern.cytoscape.NetworkChecker

initialize(Network) - Method in interface fern.analysis.NetworkSearchAction

Gets called before anything is inserted into the search structure.

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

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

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

initialize(double[]) - Method in class fern.simulation.algorithm.GroupContainer

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

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

Initializes the algorithm: set t=0reset the AmountManagerrecalculate the propensities Gets called at the very beginning of start

InstantOutputObserver - Class in fern.simulation.observer

Simply prints out every event that the simulator reports to the observer.

InstantOutputObserver(Simulator, PrintWriter) - Constructor for class fern.simulation.observer.InstantOutputObserver

Creates the observer for a given simulator and a given PrintWriter

interpolateLinear(double, double[], double[]) - Static method in class fern.tools.NumberTools

Performs a linear interpolation of the values.

interpolateLinear(double, double, double, double, double) - Static method in class fern.tools.NumberTools

Interpolates a value

IntervalObserver - Class in fern.simulation.observer

Base class for observing certain aspects repeatedly after a given interval.

IntervalObserver(Simulator, double, String[]) - Constructor for class fern.simulation.observer.IntervalObserver

Create the observer for a given simulator, a given interval, given indices with names.

IntQueue - Class in fern.analysis

IntQueue is an search structure for AnalysisBase representing an fifo queue for a breadth first search.

IntQueue() - Constructor for class fern.analysis.IntQueue

IntQueue(int) - Constructor for class fern.analysis.IntQueue

IntSearchStructure - Interface in fern.analysis

Implementing class can be used as search structure for searches in AnalysisBase.

IntStack - Class in fern.analysis

IntStack is an search structure for AnalysisBase representing an lifo stack for a depth first search.

IntStack() - Constructor for class fern.analysis.IntStack

IntStack(int) - Constructor for class fern.analysis.IntStack

inverse(String[]) - Static method in class fern.tools.NumberTools

Inverts the given array in place and returns it.

IrreversibleIsomerization - Class in fern.example

Uses the Irreversible-isomerization model to show effects of different choices for epsilon.

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

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

Returns whether or not gnuplot is accessible

isAutocatalyticReaction(int) - Method in class fern.analysis.AutocatalyticNetworkDetection

Returns true if the given reaction is autocatalytic.

isAutocatalyticSpecies(int) - Method in class fern.analysis.AutocatalyticNetworkDetection

Returns true if the given species is autocatalytic.

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

Gets whether or not to count the number of random number generations

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

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

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

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

Gets whether the amount values are returned interpolated for theta events.

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

Gets whether or not to plot quality data.

isReactionNode(Node) - Method in interface fern.cytoscape.NetworkChecker.NodeClassifier

isReactionNode(Node) - Method in class fern.cytoscape.NetworkChecker.NodeClassifierByAnnotation

isReactionToProductEdge(Edge) - Method in interface fern.cytoscape.NetworkChecker.EdgeClassifier

isReactionToProductEdge(Edge) - Method in class fern.cytoscape.NetworkChecker.EdgeClassifierByDirection

isReactionToProductEdge(Edge) - Method in class fern.cytoscape.NetworkChecker.EdgeClassifierByIdentifier

isReactionToReactantEdge(Edge) - Method in interface fern.cytoscape.NetworkChecker.EdgeClassifier

isReactionToReactantEdge(Edge) - Method in class fern.cytoscape.NetworkChecker.EdgeClassifierByDirection

isReactionToReactantEdge(Edge) - Method in class fern.cytoscape.NetworkChecker.EdgeClassifierByIdentifier

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

isSpeciesNode(Node) - Method in interface fern.cytoscape.NetworkChecker.NodeClassifier

isSpeciesNode(Node) - Method in class fern.cytoscape.NetworkChecker.NodeClassifierByAnnotation

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

Using theta method means that the time intervals are registered at the simulator and the simulator invokes at this moment the method theta.

isUsable() - Method in interface fern.cytoscape.NetworkChecker.EdgeClassifier

isUsable() - Method in class fern.cytoscape.NetworkChecker.EdgeClassifierByDirection

isUsable() - Method in class fern.cytoscape.NetworkChecker.EdgeClassifierByIdentifier

isUsable() - Method in interface fern.cytoscape.NetworkChecker.NodeClassifier

isUsable() - Method in class fern.cytoscape.NetworkChecker.NodeClassifierByAnnotation

isUsable() - Method in class fern.cytoscape.NetworkChecker.NodeParameter

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

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

Gets if each step is to print to stdout.

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

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

Yields the tab separated columns row by row.

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

Yields the tab separated columns row by row.

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

Yields the tab separated columns row by row.