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

C

calculate(AmountManager, Simulator) - Method in class fern.network.sbml.MathTree

Evaluate the MathTree.

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

Calculates the histogram distance of two histograms.

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

Calculates partial differentials of the propensity functions for the tau leaping methods.

calculatePartialDerivative(int, AmountManager, int, double) - Method in interface fern.network.PartialDerivativePropensityCalculator

Calculates partial differentials of the propensity functions for the tau leaping methods.

calculatePropensity(int, AmountManager, Simulator) - Method in class fern.cellDesigner.CellDesignerPropensityCalculator

calculatePropensity(int, AmountManager, Simulator) - Method in class fern.network.AbstractKineticConstantPropensityCalculator

Calculates the propensity for reaction by the formula h*c, where c is the kinetic constant for reaction and h is the number of distinct molecular reactant combinations for reaction.

calculatePropensity(int, AmountManager, Simulator) - Method in interface fern.network.PropensityCalculator

Calculates the propensity for a reaction given the amounts of the AmountManager.

calculatePropensity(int, AmountManager, Simulator) - Method in class fern.network.sbml.SBMLPropensityCalculator

CatalysedNetwork - Class in fern.network.modification

Modifies the network by adding reactions X+C -> Y+C (where C is each catalyst of the original reaction).

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

Create a catalyzed network from an original network.

CatalystIterator - Interface in fern.network.creation

A CatalystIterator is used to enumerate the catalysts of a reaction in an AutocatalyticNetwork.

CATALYSTS_FIELD - Static variable in class fern.network.creation.AutocatalyticNetwork

Name of the field where catalysts are stored.

CATALYSTS_FIELD_REVERSIBLE - Static variable in class fern.network.creation.AutocatalyticNetwork

Name of the field where catalysts for the reverse reactions are stored.

CellDesignerNetworkWrapper - Class in fern.cellDesigner

CellDesignerNetworkWrapper(PluginModel) - Constructor for class fern.cellDesigner.CellDesignerNetworkWrapper

CellDesignerPropensityCalculator - Class in fern.cellDesigner

Propensity calculator which is used for SBMLNetworks.

CellDesignerPropensityCalculator(PluginModel, CellDesignerNetworkWrapper) - Constructor for class fern.cellDesigner.CellDesignerPropensityCalculator

Creates the MathTrees and parses the parameters.

CellGrowthObserver - Class in fern.example

Does not observe anything, but it controls the reaction networks cell.

CellGrowthObserver(Simulator, double, double) - Constructor for class fern.example.CellGrowthObserver

Creates the observer for given simulator, generation time and a time offset (because the simulator starts at time 0 and for one example it actually starts at time 1000)

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

checkReaction(int, NetworkSearchAction.NeighborType) - Method in interface fern.analysis.NetworkSearchAction

Gets called, before the reaction is inserted into the search structure.

checkReactionNode(Network, int) - Method in interface fern.analysis.NodeChecker

checkReactionNode(Network, int) - Method in class fern.analysis.NodeCheckerByAnnotation

checkSpecies(int, NetworkSearchAction.NeighborType) - Method in interface fern.analysis.NetworkSearchAction

Gets called, before the species is inserted into the search structure.

checkSpeciesNode(Network, int) - Method in interface fern.analysis.NodeChecker

checkSpeciesNode(Network, int) - Method in class fern.analysis.NodeCheckerByAnnotation

Children - Variable in class fern.network.sbml.MathTree.InnerNode

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

Clears all collected benchmark data.

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

Clears the loaded data.

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

coefficient - Variable in class fern.cytoscape.NetworkChecker

CollectionAxes - Class in fern.tools.gnuplot

Implementation of Axes to use with Collections or Iterables of any number type or array of numbers (the type of the collection is inferred by using the reflection api).

CollectionAxes(Collection) - Constructor for class fern.tools.gnuplot.CollectionAxes

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

CollectionAxes(Iterable) - Constructor for class fern.tools.gnuplot.CollectionAxes

Create a new Axes object containing a collection (which is copied from the given iterable) without labels /styles.

CollectionAxes(Collection, String[], String[]) - Constructor for class fern.tools.gnuplot.CollectionAxes

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

CollectionAxes(Iterable, String[], String[]) - Constructor for class fern.tools.gnuplot.CollectionAxes

Create a new Axes object containing a collection (which is copied from the given iterable) with the given labels /styles (either can be null).

ColorCalculator - Class in fern.cytoscape

ColorCalculator() - Constructor for class fern.cytoscape.ColorCalculator

colorCalculator - Static variable in class fern.cytoscape.FernVisualStyle

ColorCalculator.Scale - Enum in fern.cytoscape

ColorPicker - Class in fern.cytoscape.ui

ColorPicker(Frame) - Constructor for class fern.cytoscape.ui.ColorPicker

ColorSpectrum - Class in fern.tools

Provides methods to assign colors to numbers between 0 and 1.

ColorSpectrum() - Constructor for class fern.tools.ColorSpectrum

ComplexDependenciesPropensityCalculator - Interface in fern.network

In a SBML network, the propensities of reaction are calculated by using the kineticLaw tag, which contains a MathML expression.

CompositionRejection - Class in fern.simulation.algorithm

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

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

CompositionRejectionStressTest - Class in fern.example

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

computePath(String, String...) - Method in class fern.analysis.ShortestPath

Compute the shortest paths from some source species to one species.

computePath(NodeChecker, String, String...) - Method in class fern.analysis.ShortestPath

Compute the shortest paths from some source species to one species by only using parts of the network specified by the NodeChecker checker.

computePaths(String...) - Method in class fern.analysis.ShortestPath

Compute all shortest paths from some source species.

computePaths(NodeChecker, String...) - Method in class fern.analysis.ShortestPath

Compute all shortest paths from some source species by only using parts of the network specified by the NodeChecker checker.

ConfigReader - Class in fern.tools

Reads simple config files for test cases and makes the data of it accessible.

ConfigReader(String) - Constructor for class fern.tools.ConfigReader

Reads the given file and stores the data.

ConstantAmountManager - Class in fern.network

ConstantAmountManager(long) - Constructor for class fern.network.ConstantAmountManager

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

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

Returns true iff the network contains an annotation of the specified type.

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

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

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

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

Returns true iff the reaction contains an annotation of the specified type.

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

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

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

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

Returns true iff the species contains an annotation of the specified type.

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

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

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

Performs a deep cast of an int[].

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

createHistogram(Collection<double[]>, int, int...) - Static method in class fern.tools.NumberTools

Creates a histogram from the given data.

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

Create a histogram for the given array.

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

Create a histogram map for the given array.

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

Creates the inverse array to the given array.

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

Creates the inverse map to the given array.

createRandomDoubleArray(int, AbstractDistribution) - Method in class fern.benchmark.Benchmark

Creates a test set containing size random numbers of the distribution dist.

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

Replaces the values in the given array with the cumulative sum of the array.

CytoscapeAnnotationManager - Class in fern.cytoscape

CytoscapeAnnotationManager(CytoscapeNetworkWrapper) - Constructor for class fern.cytoscape.CytoscapeAnnotationManager

CytoscapeColorChangeObserver - Class in fern.cytoscape

CytoscapeColorChangeObserver(boolean, boolean, Simulator, CytoscapeNetworkWrapper, FernVisualStyle, String[], double) - Constructor for class fern.cytoscape.CytoscapeColorChangeObserver

CytoscapeNetworkWrapper - Class in fern.cytoscape

CytoscapeNetworkWrapper(NetworkChecker, CyNetwork, CyNetworkView, CyAttributes) - Constructor for class fern.cytoscape.CytoscapeNetworkWrapper

CytoscapeVisualizer - Class in fern.cytoscape

CytoscapeVisualizer() - Constructor for class fern.cytoscape.CytoscapeVisualizer

CytoscapeVisualizer.ShowMainFrameAction - Class in fern.cytoscape

CytoscapeVisualizer.ShowMainFrameAction() - Constructor for class fern.cytoscape.CytoscapeVisualizer.ShowMainFrameAction

CytoscapeVisualizer.SimulationAction - Class in fern.cytoscape

CytoscapeVisualizer.SimulationAction() - Constructor for class fern.cytoscape.CytoscapeVisualizer.SimulationAction