Index (Systems Biology Simulation Core Library (SBSCL) 2.1 API)

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

A

a21 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
a31 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
a32 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
a41 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
a42 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
a43 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
a51 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
a52 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
a53 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
a54 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
aborted(double) - Method in class org.simulator.math.odes.EventInProgress: The event has been aborted between trigger and execution.
aborted(double) - Method in class org.simulator.sbml.SBMLEventInProgressWithDelay
About - Class in org.simulator: This class displays a short about message for this library.
About() - Constructor for class org.simulator.About
abs(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
ABSOLUTE - Static variable in class org.testsuite.SBMLTestSuiteRunnerWrapper
AbstractBaseTauLeaping - Class in fern.simulation.algorithm: Base class for all tau leaping procedures (which are different in the methods choosing the timestep candidates for critical and noncritical reactions).
AbstractBaseTauLeaping(Network) - Constructor for class fern.simulation.algorithm.AbstractBaseTauLeaping: Create the simulator for a given network.
AbstractDESSolver - Class in org.simulator.math.odes: This Class represents an abstract solver for event-driven DES
AbstractDESSolver() - Constructor for class org.simulator.math.odes.AbstractDESSolver: Initialize with default integration step size and non-negative attribute true.
AbstractDESSolver(AbstractDESSolver) - Constructor for class org.simulator.math.odes.AbstractDESSolver: Clone constructor.
AbstractDESSolver(double) - Constructor for class org.simulator.math.odes.AbstractDESSolver: Initialize with given integration step size.
AbstractDESSolver(double, boolean) - Constructor for class org.simulator.math.odes.AbstractDESSolver: Initialize with given step size and a flag whether or not negative values should be allowed.
AbstractKineticConstantPropensityCalculator - Class in fern.network: Base implementation of a PropensityCalculator.
AbstractKineticConstantPropensityCalculator(int[][]) - Constructor for class fern.network.AbstractKineticConstantPropensityCalculator: Creates a AbstractKineticConstantPropensityCalculator by an array of adjacency arrays for the reaction's reactant species (which are the only one needed for the propensity calculation).
AbstractNetworkImpl - Class in fern.network: Base implementation for the Network interface.
AbstractNetworkImpl(String) - Constructor for class fern.network.AbstractNetworkImpl: Create the network and give it an identifier.
AbstractTauLeapingPropensityBoundSimulator - 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.
AbstractTauLeapingPropensityBoundSimulator(Network) - Constructor for class fern.simulation.algorithm.AbstractTauLeapingPropensityBoundSimulator
activateReaction(int, double, Simulator.FireType, int) - Method in class fern.example.CellGrowthObserver
activateReaction(int, double, Simulator.FireType, int) - Method in class fern.network.sbml.SBMLEventHandlerObserver
activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.AmountAtMomentObserver: Do nothing
activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.FireTypeObserver: Counts the firing for the given Simulator.FireType
activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.InstantOutputObserver: Prints event.
activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.IntervalObserver: Do nothing.
activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.LeapObserver: Do nothing.
activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.Observer: Gets called before a reaction fires.
activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.RandomNumberGeneratorCallObserver: Do nothing.
activateReaction(int, double, Simulator.FireType, int) - Method in class fern.simulation.observer.ReactionIntervalObserver: Record the firing of mu, if mu is registered.
AdamsBashforthSolver - Class in org.simulator.math.odes: This class is a wrapper for the Adams-Bashforth solver in the Apache Math Library.
AdamsBashforthSolver() - Constructor for class org.simulator.math.odes.AdamsBashforthSolver: default constructor
AdamsBashforthSolver(AdamsBashforthSolver) - Constructor for class org.simulator.math.odes.AdamsBashforthSolver: Clone constructor
AdamsBashforthSolver(double) - Constructor for class org.simulator.math.odes.AdamsBashforthSolver
AdamsBashforthSolver(double, boolean) - Constructor for class org.simulator.math.odes.AdamsBashforthSolver
AdamsMoultonSolver - Class in org.simulator.math.odes: This class is a wrapper for the Adams-Moulton solver in the Apache Math Library.
AdamsMoultonSolver() - Constructor for class org.simulator.math.odes.AdamsMoultonSolver
AdamsMoultonSolver(AdamsMoultonSolver) - Constructor for class org.simulator.math.odes.AdamsMoultonSolver: clone constructor
AdamsMoultonSolver(double) - Constructor for class org.simulator.math.odes.AdamsMoultonSolver
AdamsMoultonSolver(double, boolean) - Constructor for class org.simulator.math.odes.AdamsMoultonSolver
AdaptiveStepsizeIntegrator - Class in org.simulator.math.odes: This is an abstract class for solvers with adaptive stepsizes and given relative and absolute tolerances.
AdaptiveStepsizeIntegrator() - Constructor for class org.simulator.math.odes.AdaptiveStepsizeIntegrator
AdaptiveStepsizeIntegrator(AdaptiveStepsizeIntegrator) - Constructor for class org.simulator.math.odes.AdaptiveStepsizeIntegrator: clone constructor
AdaptiveStepsizeIntegrator(double) - Constructor for class org.simulator.math.odes.AdaptiveStepsizeIntegrator
AdaptiveStepsizeIntegrator(double, boolean) - Constructor for class org.simulator.math.odes.AdaptiveStepsizeIntegrator
add(int) - Method in interface fern.analysis.IntSearchStructure
addAssignment(int, double) - Method in class org.simulator.math.odes.EventInProgress: Adds an event assignment.
addAxes(Axes) - Method in class fern.tools.gnuplot.Axes: Attaches an Axes object to this one.
addBlock(String[]) - Method in class org.simulator.math.odes.MultiTable: Creates a new MultiTable.Block and adds it to this object.
addCommand(String...) - Method in class fern.tools.gnuplot.GnuPlot: Adds commands to the list of commands which are given to gnuplot by invoking plot
addConstraintListener(ConstraintListener) - Method in class org.simulator.sbml.EquationSystem: Adds the given ConstraintListener to this interpreter's list of listeners.
addData(double[]) - Method in class fern.benchmark.Benchmark: Adds benchmark data to the data pool.
addData(Collection, String[], String[]) - Method in class fern.tools.gnuplot.GnuPlot: Adds data in order to plot it.
addData(Axes) - Method in class fern.tools.gnuplot.GnuPlot: Adds data in order to plot it.
addData(Object, String[], String[]) - Method in class fern.tools.gnuplot.GnuPlot: Adds data in order to plot it.
addData(Object[], boolean, String[], String[]) - Method in class fern.tools.gnuplot.GnuPlot: Adds data in order to plot it.
addEqualsConstraint(LinearEqualsConstraint) - Method in class org.simulator.fba.NewGLPKSolver
Additional - Static variable in class fern.tools.gnuplot.Axes
addLinearBiggerThanEqualsConstraint(LinearBiggerThanEqualsConstraint) - Method in class org.simulator.fba.NewGLPKSolver
addLinearSmallerThanEqualsConstraint(LinearSmallerThanEqualsConstraint) - Method in class org.simulator.fba.NewGLPKSolver
AddMetaInfo - Class in org.simulator.sbml: This class contains static methods to add meta information to a model inside SBMLDocument.
AddMetaInfo() - Constructor for class org.simulator.sbml.AddMetaInfo
addObserver(Observer) - Method in class fern.simulation.Simulator: Adds an observer to the list of observers.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.simulator.math.odes.AbstractDESSolver
addPropertyChangeListener(PropertyChangeListener) - Method in interface org.simulator.math.odes.DESSolver: Add PropertyChangedListener to this Solver
addRuleObject(AssignmentRuleValue) - Method in class org.simulator.sbml.SBMLEventInProgress: Adds the math of an assignment rule as an AssignmentRuleObject.
addValues(Double[], double) - Method in class org.simulator.math.odes.EventInProgress: The event associated with this class has been triggered.
addValues(Double[], double) - Method in class org.simulator.sbml.SBMLEventInProgressWithDelay
ALF - Static variable in class org.simulator.math.MatrixOperations: Ensures sufficient decrease in function value
AlgebraicRuleConverter - Class in org.simulator.sbml: This class converts the algebraic rules of a model to assignment rules based on the given matching.
AlgebraicRuleConverter(Map<SBase, SBase>, Model) - Constructor for class org.simulator.sbml.AlgebraicRuleConverter: Creates a new AlgebraicRuleConverter for the given matching and model
AMOUNT - Static variable in class org.testsuite.SBMLTestSuiteRunnerWrapper
AmountAtMomentObserver - Class in fern.simulation.observer: Observes the amount of some molecule species at a certain moment.
AmountAtMomentObserver(Simulator, double, String...) - Constructor for class fern.simulation.observer.AmountAtMomentObserver: Creates the observer for the given simulator, the given theta and the given species
AmountAtMomentObserver(Simulator, double, int...) - Constructor for class fern.simulation.observer.AmountAtMomentObserver: Creates the observer for the given simulator, the given theta and the given species
AmountIntervalObserver - Class in fern.simulation.observer: Observes amounts of molecule species repeatedly after certain intervals.
AmountIntervalObserver(Simulator, double, int...) - Constructor for class fern.simulation.observer.AmountIntervalObserver: Creates the observer for a given simulator, a given interval and given species indices
AmountIntervalObserver(Simulator, double, String...) - Constructor for class fern.simulation.observer.AmountIntervalObserver: Creates the observer for a given simulator, a given interval and given species names.
AmountIntervalObserver(Simulator, double, int, String...) - Constructor for class fern.simulation.observer.AmountIntervalObserver: Creates the observer for a given simulator, a given interval and given species names with total simulation time.
AmountLowerThanController - Class in fern.simulation.controller
AmountLowerThanController(long, String) - Constructor for class fern.simulation.controller.AmountLowerThanController
AmountLowerThanController(long, int) - Constructor for class fern.simulation.controller.AmountLowerThanController
AmountManager - Interface in fern.network: The AmountManager is one of the most important connections between a Network and a Simulator.
AnalysisBase - Class in fern.analysis: This class can be used as a base class for many analysis algorithms (like AutocatalticNetworkDetection, ShortestPath, ...).
AnalysisBase(Network) - Constructor for class fern.analysis.AnalysisBase: Creates an analysis instance.
and(ASTNodeValue[], int, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
AndController - Class in fern.simulation.controller: Implements a SimulationController composed of many SimulationController.
AndController(SimulationController...) - Constructor for class fern.simulation.controller.AndController
annotate(String, String) - Method in class fern.analysis.AutocatalyticNetworkDetection: Adds annotations to each autocatalytic reaction / species.
AnnotationManager - Interface in fern.network: AnnotationManager objects are the places, where static (or quasi-static) properties of a network are stored.
AnnotationManagerImpl - Class in fern.network: Base implementation of the AnnotationManager interface.
AnnotationManagerImpl() - Constructor for class fern.network.AnnotationManagerImpl
applyDefaultStyle(String) - Method in class fern.tools.gnuplot.Axes: Sets the style of each column to the default style except for columns that already have a style.
arccos(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
arccosh(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
arccot(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
arccoth(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
arccsc(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
arccsch(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
arcsec(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
arcsech(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
arcsin(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
arcsinh(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
arctan(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
arctanh(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
areEqual(Network, Network) - Static method in class fern.tools.NetworkTools: Gets whether or not the two given networks contain the same species, the same reactions and yield the same propensities when the amounts of each reactant are respectively 1, 5, 10, 100.
argMax(Map<Integer, Integer>) - Static method in class fern.tools.NumberTools: Gets the argmax of the given map.
ArithmeticMean - Class in org.simulator.math: Class that computes the arithmetic mean of the given column distances.
ArithmeticMean() - Constructor for class org.simulator.math.ArithmeticMean
ArrayKineticConstantPropensityCalculator - Class in fern.network: Implementation of an AbstractKineticConstantPropensityCalculator which uses an array to store the constants for each reaction.
ArrayKineticConstantPropensityCalculator(int[][], double[]) - Constructor for class fern.network.ArrayKineticConstantPropensityCalculator: Create the propensity calculator with given constants and given reactant adjacency arrays
ArrayMatrixAxes - Class in fern.tools.gnuplot: Implementation of Axes to use with array matrixes of any number type (the type of the arrays is inferred by using the reflection api).
ArrayMatrixAxes(Object) - Constructor for class fern.tools.gnuplot.ArrayMatrixAxes: Create a new Axes object containing the given array matrix without labels / styles.
ArrayMatrixAxes(Object, String[], String[]) - Constructor for class fern.tools.gnuplot.ArrayMatrixAxes: Create a new Axes object containing the given array matrix with the given labels /styles (either can be null).
AssignmentRuleValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of an AssignmentRule together with the variable of the rule.
AssignmentRuleValue(ASTNodeValue, int) - Constructor for class org.simulator.sbml.astnode.AssignmentRuleValue
AssignmentRuleValue(ASTNodeValue, String, Map<String, Double>) - Constructor for class org.simulator.sbml.astnode.AssignmentRuleValue: Constructor for rules that refer to a species reference
AssignmentRuleValue(ASTNodeValue, int, Species, int, boolean, SBMLValueHolder, boolean) - Constructor for class org.simulator.sbml.astnode.AssignmentRuleValue: Constructor for rules that refer to a species
ASTNodeInterpreter - Class in org.simulator.sbml.astnode: This class is an efficient ASTNodeInterpreter that takes the time of the calculation into account.
ASTNodeInterpreter(SBMLValueHolder) - Constructor for class org.simulator.sbml.astnode.ASTNodeInterpreter
ASTNodeValue - Class in org.simulator.sbml.astnode: This class can compute and store the interpreted value (double or boolean) of an ASTNode at the current time.
ASTNodeValue(EquationSystem, ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.ASTNodeValue
ASTNodeValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.ASTNodeValue
AutocatalyticNetwork - Class in fern.network.creation: Evolve an autocatalytic network.
AutocatalyticNetwork(char[], Probability, Probability, int) - Constructor for class fern.network.creation.AutocatalyticNetwork: Creates the autocatalytic network from given monomers, reaction probability, catalysis probability up to a given polymer length.
AutocatalyticNetwork(char[], Probability, Probability, int, boolean) - Constructor for class fern.network.creation.AutocatalyticNetwork: Creates the autocatalytic network from given monomers, reaction probability, catalysis probability up to a given polymer length. useDefault should usually set to true unless you want to evolve really huge networks.
AutocatalyticNetworkDetection - Class in fern.analysis: Detects the autocatalytic set of the given network if there is any.
AutocatalyticNetworkDetection(Network) - Constructor for class fern.analysis.AutocatalyticNetworkDetection: Creates the AutocatalyticDetection by using the in the network built in CatalystIterator.
AutocatalyticNetworkDetection(Network, CatalystIterator) - Constructor for class fern.analysis.AutocatalyticNetworkDetection: Creates the AutocatalyticDetection by using the second argument as CatalystIterator.
AutocatalyticNetworkExample - Class in fern.example: Here, the evolution of a reaction network as proposed by [1] is performed.
AutocatalyticNetworkExample() - Constructor for class fern.example.AutocatalyticNetworkExample
avg(double[]) - Static method in class fern.tools.NumberTools: Gets the avg of the array
Axes - Class in fern.tools.gnuplot: Contains the data columns for GnuPlot.
Axes() - Constructor for class fern.tools.gnuplot.Axes

B

balance(double[][]) - Static method in class org.simulator.math.MatrixOperations: Given a matrix a[1..n][1..n], this routine replaces it by a balanced matrix with identical eigenvalues.
Benchmark - Class in fern.benchmark: Base class for all benchmark classes.
Benchmark() - Constructor for class fern.benchmark.Benchmark
benchmark() - Method in class fern.benchmark.SimulatorPerformance: Performs one benchmark for each of the six simulators.
benchmarkLangevinAgainstTauLeapNumberGeneration(double[]) - Method in class fern.benchmark.RandomNumber: Benchmark for the different computation of random numbers in the Langevin (normal distributed) and tau leap (poisson distributed) method for double values at
bfs(int[], int[], NetworkSearchAction) - Method in class fern.analysis.AnalysisBase: Performs a breath first search starting at the given sources (which means the contents of speciesSource and reactionSource are the initial content of the queue.
BiomodelsExample - Class in org.simulator.examples: This class can test the simulation of all models from BioModels database.
BiomodelsExample() - Constructor for class org.simulator.examples.BiomodelsExample

C

c2 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c21 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c3 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c31 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c32 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c4 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c41 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c42 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c43 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c51 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c52 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c53 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c54 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c61 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c62 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c63 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c64 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
c65 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
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.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.
ceiling(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
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)
changePriority(double) - Method in class org.simulator.sbml.SBMLEventInProgress: Change the priority.
changeRate - Variable in class org.simulator.sbml.EquationSystem: An array that stores derivatives of each species in the model system at current time.
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
clearAssignments() - Method in class org.simulator.math.odes.EventInProgress: Clears all event assignments.
clearData() - Method in class fern.benchmark.Benchmark: Clears all collected benchmark data.
clearData() - Method in class fern.tools.gnuplot.GnuPlot: Clears the loaded data.
clearRuleObjects() - Method in class org.simulator.sbml.SBMLEventInProgress: Clears the assignment rule objects.
clone() - Method in class org.simulator.math.odes.AbstractDESSolver
clone() - Method in class org.simulator.math.odes.AdamsBashforthSolver
clone() - Method in class org.simulator.math.odes.AdamsMoultonSolver
clone() - Method in interface org.simulator.math.odes.DESSolver
clone() - Method in class org.simulator.math.odes.DormandPrince54Solver
clone() - Method in class org.simulator.math.odes.DormandPrince853Solver
clone() - Method in class org.simulator.math.odes.EulerMethod
clone() - Method in class org.simulator.math.odes.FirstOrderSolver
clone() - Method in class org.simulator.math.odes.GraggBulirschStoerSolver
clone() - Method in class org.simulator.math.odes.HighamHall54Solver
clone() - Method in class org.simulator.math.odes.RosenbrockSolver
clone() - Method in class org.simulator.math.odes.RungeKutta_EventSolver
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).
ColorSpectrum - Class in fern.tools: Provides methods to assign colors to numbers between 0 and 1.
ColorSpectrum() - Constructor for class fern.tools.ColorSpectrum
CompartmentOrParameterValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to a Compartment or a Parameter.
CompartmentOrParameterValue(ASTNodeInterpreter, ASTNode, Symbol, SBMLValueHolder, int) - Constructor for class org.simulator.sbml.astnode.CompartmentOrParameterValue
CompExample - Class in org.simulator.examples: A simple program that performs a simulation of SBML files containing hierarchical models.
CompExample() - Constructor for class org.simulator.examples.CompExample
compile(double, int, String) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
compile(double, String) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
compileBoolean(CallableSBase, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
compileBoolean(double) - Method in class org.simulator.sbml.astnode.ASTNodeValue: Computes the boolean value if the time has changed and otherwise returns the already computed value
compileDouble(String, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
compileDouble(CallableSBase, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
compileDouble(double, double) - Method in class org.simulator.sbml.astnode.ASTNodeValue: Computes the double value if the time has changed and otherwise returns the already computed value
compileDouble(double, double) - Method in class org.simulator.sbml.astnode.LocalParameterValue
compileDouble(double) - Method in class org.simulator.sbml.astnode.StoichiometryValue: Computes the value of the stoichiometry at the current time if it has not been computed yet or is not constant.
compileReaction(int) - Method in class org.simulator.sbml.SBMLinterpreter
compileString(ASTNodeValue) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
compileString(ASTNode) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
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
CompSimulator - Class in org.simulator.comp: Class for simulating models encoded in the SBML comp package.
CompSimulator(File) - Constructor for class org.simulator.comp.CompSimulator: Constructor for the CompSimulator class.
computeChange(DESystem, double[], double, double, double[], boolean) - Method in class org.simulator.math.odes.AbstractDESSolver: Computes the change for a given system at the current time with the current setting for the integration step size.
computeChange(DESystem, double[], double, double, double[], boolean) - Method in class org.simulator.math.odes.EulerMethod
computeChange(DESystem, double[], double, double, double[], boolean) - Method in class org.simulator.math.odes.FirstOrderSolver
computeChange(DESystem, double[], double, double, double[], boolean) - Method in class org.simulator.math.odes.RosenbrockSolver
computeChange(DESystem, double[], double, double, double[], boolean) - Method in class org.simulator.math.odes.RungeKutta_EventSolver
computeDelayedValue(double, String, DESystem, double[], int) - Method in class org.simulator.math.odes.AbstractDESSolver
computeDelayedValue(double, String, DESystem, double[], int) - Method in interface org.simulator.math.odes.DelayValueHolder: Returns the value for the element with the given id at a time point in the past, where the time gives the amount of time in the past.
computeDelayedValue(double, String, DESystem, double[], int) - Method in class org.simulator.sbml.EquationSystem
computeDerivatives(double, double[], double[]) - Method in class org.simulator.sbml.SBMLinterpreter
computeDerivativeWithChangingCompartment(Species, double[]) - Method in class org.simulator.sbml.SBMLinterpreter
computeMean(double...) - Method in class org.simulator.math.ArithmeticMean: Computes the overall distance
computeMean(double...) - Method in class org.simulator.math.DistanceSum: Computes the overall distance
computeMean(double...) - Method in class org.simulator.math.MeanFunction: Computes the overall distance
computeMean(List<Double>) - Method in class org.simulator.math.MeanFunction: Computes the overall distance
computeMean(Iterable<? extends Number>) - Method in class org.simulator.math.MeanFunction: Computes the overall distance
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.
CONCENTRATION - Static variable in class org.testsuite.SBMLTestSuiteRunnerWrapper
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.
Constant(double) - Constructor for class fern.tools.functions.Probability.Constant
ConstantAmountManager - Class in fern.network
ConstantAmountManager(long) - Constructor for class fern.network.ConstantAmountManager
CONSTRAINT_VIOLATION_LOG - Static variable in interface org.simulator.sbml.ConstraintListener: Key to memorize user objects for logging the constraint violation
ConstraintEvent - Class in org.simulator.sbml: This class represents the violation of a Constraint during simulation.
ConstraintEvent(Constraint, double) - Constructor for class org.simulator.sbml.ConstraintEvent: Creates a new ConstraintEvent for the given Constraint and the given point in time.
ConstraintExample - Class in org.simulator.examples: This class tests the ConstraintListener interface implementation SimpleConstraintListener by evaluating a simple test model that contains a Constraint.
ConstraintExample() - Constructor for class org.simulator.examples.ConstraintExample
ConstraintListener - Interface in org.simulator.sbml: A listener interface that allows the processing of Constraints that triggered during simulation.
containsColumn(String) - Method in class org.simulator.math.odes.MultiTable.Block: Checks whether or not this MultiTable.Block contains a MultiTable.Block.Column with the given identifier.
containsEventsOrRules() - Method in interface org.simulator.math.odes.DESystem: This method is used to check if this differential equation system contains any events or rules that would require a special treatment by the numerical solver.
containsEventsOrRules() - Method in class org.simulator.sbml.EquationSystem: This method is used to check if this differential equation system contains any events or rules that would require a special treatment by the numerical solver.
containsFastProcesses() - Method in interface org.simulator.math.odes.FastProcessDESystem
containsFastProcesses() - Method in class org.simulator.sbml.EquationSystem
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 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
containsSBMLModel() - Method in class org.simulator.omex.OMEXArchive
containsSEDMLDescp() - Method in class org.simulator.omex.OMEXArchive
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[].
copyAST(ASTNode, boolean, FunctionValue, List<ASTNode>) - Method in class org.simulator.sbml.EquationSystem: Creates a copy of an ASTNode or returns an ASTNode that is equal to the presented node.
cos(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
cosh(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
cot(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
coth(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
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.
createIntegrator() - Method in class org.simulator.math.odes.AdamsBashforthSolver
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.
csc(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
csch(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
CSVImporter - Class in org.simulator.io: This class is for importing CSV files.
CSVImporter() - Constructor for class org.simulator.io.CSVImporter
cumSum(int[]) - Static method in class fern.tools.NumberTools: Replaces the values in the given array with the cumulative sum of the array.

D

d1 - Static variable in class org.simulator.math.odes.RosenbrockSolver
d2 - Static variable in class org.simulator.math.odes.RosenbrockSolver
d3 - Static variable in class org.simulator.math.odes.RosenbrockSolver
d4 - Static variable in class org.simulator.math.odes.RosenbrockSolver
DecayingDimerizingHistogramDistances - Class in fern.example: Demonstration of performance and accuracy differences of the different simulation algorithms.
DecayingDimerizingHistogramDistances() - Constructor for class fern.example.DecayingDimerizingHistogramDistances
DecayingDimerizingInteractive - Class in fern.example: Demonstration of performance and accuracy differences of the different simulation algorithms.
DecayingDimerizingInteractive() - Constructor for class fern.example.DecayingDimerizingInteractive
DecayingDimerizingPlots - Class in fern.example: Deprecated.
DecayingDimerizingPlots() - Constructor for class fern.example.DecayingDimerizingPlots: Deprecated.
DefaultAmountManager - Class in fern.network: Default implementation of an amount manager, that stores the amounts in arrays.
DefaultAmountManager(Network) - Constructor for class fern.network.DefaultAmountManager: Creates an AmountManager for a given network
DefaultController - Class in fern.simulation.controller: The probably most common implementation of an SimulationController.
DefaultController(double) - Constructor for class fern.simulation.controller.DefaultController: Creates the controller for a given time where the simulation has to stop.
delay(ASTNodeValue, ASTNodeValue, String, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
DelayedDESystem - Interface in org.simulator.math.odes: This interface describes a differential equation system containing values with a delay function.
DelayValueHolder - Interface in org.simulator.math.odes: This interface describes a value holder that can compute values with delay.
DependencyGraph - Class in fern.simulation.algorithm: Implements a dependency graph.
DependencyGraph(Network) - Constructor for class fern.simulation.algorithm.DependencyGraph: Creates the dependency graph for a given network
DESSolver - Interface in org.simulator.math.odes: A DESSolver provides algorithm for the numerical simulation of given DESystems.
DESystem - Interface in org.simulator.math.odes: A differential equation system describes how to compute the rate of change at a given state of the system.
detect() - Method in class fern.analysis.AutocatalyticNetworkDetection: Performs the detection algorithm.
dfs(int[], int[], NetworkSearchAction) - Method in class fern.analysis.AnalysisBase: Performs a depth first search starting at the given sources (which means the contents of speciesSource and reactionSource are the initial content of the stack.
distance(MultiTable.Block.Column, MultiTable.Block.Column, double) - Method in class org.simulator.math.MaxAbsDistance
distance(MultiTable.Block.Column, MultiTable.Block.Column, double) - Method in class org.simulator.math.MaxDivergenceTolerance: Returns the distance of the two vectors x and y with the given root.
distance(MultiTable.Block.Column, MultiTable.Block.Column, double) - Method in class org.simulator.math.N_Metric
distance(MultiTable.Block.Column, MultiTable.Block.Column, double) - Method in class org.simulator.math.PearsonCorrelation
distance(MultiTable.Block.Column, MultiTable.Block.Column) - Method in class org.simulator.math.QualityMeasure: Returns the distance of the two vectors x and y where the currently set root is used.
distance(MultiTable.Block.Column, MultiTable.Block.Column, double) - Method in class org.simulator.math.QualityMeasure: Returns the distance of the two vectors x and y with the given root.
distance(MultiTable, MultiTable) - Method in class org.simulator.math.QualityMeasure
distance(MultiTable.Block.Column, MultiTable.Block.Column, double) - Method in class org.simulator.math.Relative_N_Metric
distance(MultiTable.Block.Column, MultiTable.Block.Column, double) - Method in class org.simulator.math.RelativeMaxDistance
DistanceSum - Class in org.simulator.math: Sets the overall distance to the sum of the column distances.
DistanceSum() - Constructor for class org.simulator.math.DistanceSum
distanceToZero(MultiTable.Block.Column, double) - Method in class org.simulator.math.MaxAbsDistance
distanceToZero(MultiTable.Block.Column, double) - Method in class org.simulator.math.N_Metric
DivideValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to a division object.
DivideValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.DivideValue
DormandPrince54Solver - Class in org.simulator.math.odes: This class is a wrapper for the Dormand-Prince-54 solver in the Apache Math Library.
DormandPrince54Solver() - Constructor for class org.simulator.math.odes.DormandPrince54Solver: default constructor
DormandPrince54Solver(DormandPrince54Solver) - Constructor for class org.simulator.math.odes.DormandPrince54Solver: clone constructor
DormandPrince54Solver(double) - Constructor for class org.simulator.math.odes.DormandPrince54Solver
DormandPrince54Solver(double, boolean) - Constructor for class org.simulator.math.odes.DormandPrince54Solver
DormandPrince853Solver - Class in org.simulator.math.odes: This class is a wrapper for the Dormand-Prince-853 solver in the Apache Math Library.
DormandPrince853Solver() - Constructor for class org.simulator.math.odes.DormandPrince853Solver: default constructor
DormandPrince853Solver(DormandPrince853Solver) - Constructor for class org.simulator.math.odes.DormandPrince853Solver: clone constructor
DormandPrince853Solver(double) - Constructor for class org.simulator.math.odes.DormandPrince853Solver
DormandPrince853Solver(double, boolean) - Constructor for class org.simulator.math.odes.DormandPrince853Solver
drawReaction(Stochastics, double[]) - Method in class fern.simulation.algorithm.GroupContainer
Dsmts - Class in fern.example: Perform a series of tests (refer to http://www.calibayes.ncl.ac.uk/Resources/dsmts).
Dsmts() - Constructor for class fern.example.Dsmts
dumpMathTree(MathTree) - Static method in class fern.tools.NetworkTools: Dumps the MathTree to stdout.
dumpMathTree(MathTree, Writer) - Static method in class fern.tools.NetworkTools: Dumps the math tree to the given Writer.
dumpNetwork(Network) - Static method in class fern.tools.NetworkTools: Dumps the network to stdout.
dumpNetwork(Network, Writer) - Static method in class fern.tools.NetworkTools: Dumps the network to the given Writer.

E

elmhes(double[][]) - Static method in class org.simulator.math.MatrixOperations: Reduces a[1..n][1..n] to upper Hessenberg form
end() - Method in class fern.benchmark.Benchmark: Gets the elapsed time since the last call of start in nanoseconds
EPS - Static variable in class org.simulator.math.MatrixOperations: Approximate square root of the JVM precision
eq(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
eqnSystem - Variable in class org.simulator.sbml.astnode.ASTNodeValue
EquationSystem - Class in org.simulator.sbml
EquationSystem(Model) - Constructor for class org.simulator.sbml.EquationSystem
EuclideanDistance - Class in org.simulator.math: Class for computation of the Euclidean distance of two vectors.
EuclideanDistance() - Constructor for class org.simulator.math.EuclideanDistance: Initializes a new object
EulerMethod - Class in org.simulator.math.odes: In this class the Euler method for integration a differential equation system is implemented.
EulerMethod() - Constructor for class org.simulator.math.odes.EulerMethod: default constructor
EulerMethod(double) - Constructor for class org.simulator.math.odes.EulerMethod
EulerMethod(double, boolean) - Constructor for class org.simulator.math.odes.EulerMethod
EulerMethod(EulerMethod) - Constructor for class org.simulator.math.odes.EulerMethod: clone constructor
EventDESystem - Interface in org.simulator.math.odes: This class represents an event-driven differential equation system
EventInProgress - Class in org.simulator.math.odes: This class represents a compilation of the values and execution times during simulation concerning events.
EventInProgress(boolean) - Constructor for class org.simulator.math.odes.EventInProgress: Creates a new EventInProcess with the given boolean value indicating whether or not it can fire at the initial time point.
eventOccurred(double, double[], boolean) - Method in class org.simulator.math.odes.AbstractDESSolver
ExamplePath - Class in fern.example: Determine the path to the example network files.
ExamplePath() - Constructor for class fern.example.ExamplePath
executed(double) - Method in class org.simulator.math.odes.EventInProgress: The event associated with this class has been executed therefore reset some values.
executed(double) - Method in class org.simulator.sbml.SBMLEventInProgressWithDelay
executeSedML(InputStream) - Method in class org.simulator.sedml.SEDMLWriter
ExecutionException - Exception in org.simulator.sedml: Runtime exception indicating that SED-ML execution has failed.
ExecutionException(String) - Constructor for exception org.simulator.sedml.ExecutionException
exists(String) - Static method in class fern.example.ExamplePath
exp(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
extractArchive(File) - Method in class org.simulator.omex.OMEXArchive: A simple method to uncompress combine archives at desired location
ExtractSubNetwork - Class in fern.network.modification: Extracts some reactions / species from a given net to form a new network.
ExtractSubNetwork(Network, BitVector, BitVector) - Constructor for class fern.network.modification.ExtractSubNetwork: Extracts a given subnet from a network.

F

fac1 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants used to adapt the stepsize according to the error in the last step (see rodas.f)
fac2 - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants used to adapt the stepsize according to the error in the last step (see rodas.f)
factorial(double) - Static method in class org.simulator.math.Mathematics: This method computes the factorial!
factorial(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
faculty(int) - Static method in class fern.tools.NumberTools: Gets the faculty
FastProcessDESystem - Interface in org.simulator.math.odes: This interface describes differential equation systems with fast processes.
FBAExample - Class in org.simulator.examples: A simple test class to demonstrate the capabilities of the FBA implementation in Simulation Core Library.
FBAExample(File) - Constructor for class org.simulator.examples.FBAExample
FeatureNotSupportedException - Exception in fern.network
FeatureNotSupportedException(String) - Constructor for exception fern.network.FeatureNotSupportedException
fern - package fern
fern.analysis - package fern.analysis
fern.benchmark - package fern.benchmark
fern.example - package fern.example
fern.network - package fern.network
fern.network.creation - package fern.network.creation
fern.network.fernml - package fern.network.fernml
fern.network.modification - package fern.network.modification
fern.network.sbml - package fern.network.sbml
fern.simulation - package fern.simulation
fern.simulation.algorithm - package fern.simulation.algorithm
fern.simulation.controller - package fern.simulation.controller
fern.simulation.observer - package fern.simulation.observer
fern.tools - package fern.tools
fern.tools.functions - package fern.tools.functions
fern.tools.gnuplot - package fern.tools.gnuplot
FernMLAnnotationManager - Class in fern.network.fernml: AnnotationManager for FernMLNetworks.
FernMLAnnotationManager(Element) - Constructor for class fern.network.fernml.FernMLAnnotationManager: Create the AnnotationManager from the root element of the jdom tree.
FernMLNetwork - Class in fern.network.fernml: A FernMLNetwork is usually loaded from a file.
FernMLNetwork(File) - Constructor for class fern.network.fernml.FernMLNetwork: Creates a FernMLNetwork from a file.
FernMLNetwork(Network) - Constructor for class fern.network.fernml.FernMLNetwork: Create a FernMLNetwork from an existing Network.
FernMLNetwork(Network, double[]) - Constructor for class fern.network.fernml.FernMLNetwork: Creates a FernMLNetwork out of an existing network (e.g., to save it to a fernml file) using explicitly given kineticConstants (when net} doesn't use KineticConstantPropensityCalculator If kineticConstants is null or to short, a default value of 1 is taken.
FileModelResolver - Class in org.simulator.sedml: This resolver will resolve relative URIs with no scheme, i.e., relative URIs to files.
FileModelResolver(String) - Constructor for class org.simulator.sedml.FileModelResolver
filter(double[]) - Method in class org.simulator.math.odes.MultiTable: Creates a multi block table only containing the values for the given timepoints (if available)
find(String) - Static method in class fern.example.ExamplePath
finished() - Method in interface fern.analysis.NetworkSearchAction: Gets called, when the search is done.
finished() - Method in class fern.example.CellGrowthObserver
finished() - Method in class fern.network.sbml.SBMLEventHandlerObserver
finished() - Method in class fern.simulation.observer.AmountAtMomentObserver: Do nothing.
finished() - Method in class fern.simulation.observer.FireTypeObserver: Calculates the average over all runs of the simulator.
finished() - Method in class fern.simulation.observer.InstantOutputObserver: Prints event.
finished() - Method in class fern.simulation.observer.IntervalObserver: Adds the recorded data to the average data pool.
finished() - Method in class fern.simulation.observer.LeapObserver: Do nothing.
finished() - Method in class fern.simulation.observer.Observer: Gets called when a simulation has finished, directly after the termination check.
finished() - Method in class fern.simulation.observer.RandomNumberGeneratorCallObserver: Calculates the average.
fired(double) - Method in class org.simulator.math.odes.EventInProgress: Associated event has triggered therefore current value of fired to true
firePropertyChange(double, double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver: Tell each listener that property value changed.
firePropertyChange(double, double, double[]) - Method in interface org.simulator.math.odes.DESSolver: Tell each listener that property value changed.
FireTypeObserver - Class in fern.simulation.observer: Observes the different types of firings.
FireTypeObserver(Simulator) - Constructor for class fern.simulation.observer.FireTypeObserver: Create the observer for the given simulator.
FirstOrderSolver - Class in org.simulator.math.odes: This class is the superclass of the wrapper classes for the solvers of the Apache Math Library.
FirstOrderSolver() - Constructor for class org.simulator.math.odes.FirstOrderSolver: default constructor
FirstOrderSolver(double) - Constructor for class org.simulator.math.odes.FirstOrderSolver
FirstOrderSolver(double, boolean) - Constructor for class org.simulator.math.odes.FirstOrderSolver
FirstOrderSolver(FirstOrderSolver) - Constructor for class org.simulator.math.odes.FirstOrderSolver: clone constructor
floor(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
FluxBalanceAnalysis - Class in org.simulator.fba: Support for Flux Balance Analysis (FBA).
FluxBalanceAnalysis(SBMLDocument) - Constructor for class org.simulator.fba.FluxBalanceAnalysis: Initializes the linear program and all data structures based on the definitions in the given SBMLDocument.
frac(int, int) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
frac(ASTNodeValue, ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
functionBoolean(String, List<ASTNodeValue>) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
functionBoolean(ASTNodeValue, List<String>, ASTNodeValue[], double[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
functionDouble(ASTNodeValue, List<String>, ASTNodeValue[], int, double[], double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
functionDouble(String, List<ASTNodeValue>, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
FunctionValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to the application of a FunctionDefinition.
FunctionValue(ASTNodeInterpreter, ASTNode, List<ASTNode>) - Constructor for class org.simulator.sbml.astnode.FunctionValue

G

g(double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver
gam - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants for solving
geq(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
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
getAbsTol() - Method in class org.simulator.math.odes.AdaptiveStepsizeIntegrator
getActiveObjective() - Method in class org.simulator.fba.FluxBalanceAnalysis: Gets the id of the active objective function
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
getAdditionalValueCount() - Method in interface org.simulator.math.odes.RichDESystem: Gives the number of intermediate results that are computed by this class.
getAdditionalValueCount() - Method in class org.simulator.sbml.EquationSystem: Gives the number of intermediate results that are computed by this class.
getAdditionalValueIds() - Method in interface org.simulator.math.odes.RichDESystem: This provides the column/row identifiers of all intermediate results: one identifier per result.
getAdditionalValueIds() - Method in class org.simulator.sbml.EquationSystem: This provides the column/row identifiers of all intermediate results: one identifier per result.
getAdditionalValues(double, double[]) - Method in interface org.simulator.math.odes.RichDESystem: Computes and/or delivers the intermediate results at the given time and for the given results from the previous time step.
getAdditionalValues(double, double[]) - Method in class org.simulator.sbml.SBMLinterpreter: Computes and/or delivers the intermediate results at the given time and for the given results from the previous time step.
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.
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.ReversibleNetwork: Gets the AmountManager for the modified network.
getAmountManager() - Method in interface fern.network.Network: Gets the AmountManager for this network.
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.ReversibleNetwork: Gets the AnnotationManager for the modified network.
getAnnotationManager() - Method in interface fern.network.Network: Gets the AnnotationManager for this network.
getArgumentValues() - Method in class org.simulator.sbml.astnode.FunctionValue: Returns the values of the arguments.
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
getAssignmentRules() - Method in class org.simulator.sbml.AlgebraicRuleConverter: Creates a list an assignment rule for every algebraic rule in the given model
getAssignments() - Method in class org.simulator.math.odes.EventInProgress: Returns all event assignments as a map.
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 ,)
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.
getAvgLog() - Method in class fern.simulation.observer.IntervalObserver
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.
getBlock(int) - Method in class org.simulator.math.odes.MultiTable
getBlockCount() - Method in class org.simulator.math.odes.MultiTable
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.
getChangeRate() - Method in class org.simulator.sbml.EquationSystem
getColumn(int) - Method in class org.simulator.math.odes.MultiTable.Block: Grants access to the specified column.
getColumn(String) - Method in class org.simulator.math.odes.MultiTable.Block: Provides access to the MultiTable.Block.Column corresponding to the given identifier.
getColumn(int) - Method in class org.simulator.math.odes.MultiTable
getColumn(String) - Method in class org.simulator.math.odes.MultiTable: Returns the column corresponding to the given identifier.
getColumnClass(int) - Method in class org.simulator.math.odes.MultiTable
getColumnCount() - Method in class org.simulator.math.odes.MultiTable.Block
getColumnCount() - Method in class org.simulator.math.odes.MultiTable
getColumnDistances(MultiTable, MultiTable) - Method in class org.simulator.math.QualityMeasure: Computes the distance of two matrices as the sum of the distances of each row.
getColumnHeaders() - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getColumnIdentifier(int) - Method in class org.simulator.math.odes.MultiTable.Block
getColumnIdentifier(int) - Method in class org.simulator.math.odes.MultiTable
getColumnIndex(String) - Method in class org.simulator.math.odes.MultiTable: Returns the index of a column for a given identifier.
getColumnName() - Method in class org.simulator.math.odes.MultiTable.Block.Column: Returns the human-readable name for this column if there is any, otherwise this will return the same value as MultiTable.Block.Column.getId().
getColumnName(int) - Method in class org.simulator.math.odes.MultiTable.Block
getColumnName(int) - Method in class org.simulator.math.odes.MultiTable
getColumnNames() - Method in class org.simulator.math.odes.MultiTable.Block
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
getConstant() - Method in class org.simulator.sbml.astnode.ASTNodeValue
getConstant() - Method in class org.simulator.sbml.astnode.IntegerValue
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| !
getConstantHash() - Method in class org.simulator.sbml.EquationSystem
getConstraintListenerCount() - Method in class org.simulator.sbml.EquationSystem
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
getCopiedAST() - Method in class fern.network.sbml.MathTree: Gets the ASTNode of this MathTree.
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.
getCurrentCompartmentSize(String) - Method in class org.simulator.sbml.EquationSystem: Returns the size of the compartment with the given id.
getCurrentCompartmentSize(String) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the size of the compartment with the given id.
getCurrentCompartmentValueOf(String) - Method in class org.simulator.sbml.EquationSystem: Returns the size of the compartment of the species with the given id.
getCurrentCompartmentValueOf(String) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the size of the compartment of the species with the given id.
getCurrentParameterValue(String) - Method in class org.simulator.sbml.EquationSystem: Returns the value of the parameter with the given id.
getCurrentParameterValue(String) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the value of the parameter with the given id.
getCurrentSpeciesValue(String) - Method in class org.simulator.sbml.EquationSystem: Returns the value of the species with the given id.
getCurrentSpeciesValue(String) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the value of the species with the given id.
getCurrentStoichiometry(String) - Method in class org.simulator.sbml.EquationSystem: Returns the value of the stoichiometry of the species reference with the given id.
getCurrentStoichiometry(String) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the value of the stoichiometry of the species reference with the given id.
getCurrentTime() - Method in class org.simulator.sbml.EquationSystem: Returns the current simulation time.
getCurrentTime() - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the current simulation time.
getCurrentValueOf(String) - Method in class org.simulator.sbml.EquationSystem: Returns the current value of the SBase with the given id.
getCurrentValueOf(int) - Method in class org.simulator.sbml.EquationSystem: Returns the current value of the Y vector at the given position.
getCurrentValueOf(String) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the current value of the SBase with the given id.
getCurrentValueOf(int) - Method in interface org.simulator.sbml.SBMLValueHolder: Returns the current value of the Y vector at the given position.
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.
getData() - Method in class org.simulator.math.odes.MultiTable.Block
getData() - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getDataByColumnId(String) - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getDataByColumnIndex(int) - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getDefaultStyle() - Method in class fern.tools.gnuplot.GnuPlot: The defaultStyle is used, when no style is defined for an column in an axes object.
getDefaultValue() - Method in class org.simulator.math.QualityMeasure: Returns the default value that is returned by the distance function in cases in which the computation of the distance is not possible.
getDelayObject() - Method in class org.simulator.sbml.SBMLEventInProgress
getDependent(int) - Method in class fern.simulation.algorithm.DependencyGraph: Gets the descendants of a reaction in the dependency graph
getDimension() - Method in class org.simulator.sbml.EquationSystem
getDimensionType() - Method in class fern.tools.gnuplot.Axes: Gets if this Axes object contains 2 or 3 dimensional data.
getDoc() - Method in class org.simulator.comp.CompSimulator
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.
getEpsilon() - Method in class org.simulator.fba.FluxBalanceAnalysis: Gets the value of the EPSILON
getEventCount() - Method in interface org.simulator.math.odes.EventDESystem: Counts the number of events in this system.
getEventCount() - Method in class org.simulator.sbml.EquationSystem: Counts the number of events in this system.
getExponential(double) - Method in class fern.tools.Stochastics: Gets a random number from the exponential distribution.
getFile() - Method in class fern.example.HistogramDistanceTestSet
getFileEntries() - Method in class org.simulator.omex.OMEXArchive
getFinalValue(int) - Method in class fern.simulation.observer.IntervalObserver: Gets the last value of the given entity.
getFireStatus(double) - Method in class org.simulator.math.odes.EventInProgress: Returns a boolean value indication if the associated event has recently been triggered / fired
getFlattenedDoc() - Method in class org.simulator.comp.CompSimulator
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.
getId() - Method in class org.simulator.math.odes.MultiTable.Block.Column: Delivers the MultiTable.Block.Column identifier of this particular column.
getIdentifiers() - Method in interface org.simulator.math.odes.DESystem: Delivers an array of Strings that describe the content of each dimension of the resulting array of this DESystem.
getIdentifiers() - Method in class org.simulator.math.odes.MultiTable.Block
getIdentifiers() - Method in class org.simulator.sbml.EquationSystem: Delivers an array of Strings that describe the content of each dimension of the resulting array of this DESystem.
getImage() - Method in class fern.tools.gnuplot.GnuPlot: Return the plotted data as image.
getIndex(String) - Method in class org.simulator.sbml.astnode.FunctionValue: Returns the index of a specific argument.
getIndex() - Method in class org.simulator.sbml.astnode.RuleValue: Returns the index of the variable in the Y vector of the value holder.
getIndexByColumnID(String) - Method in class org.simulator.sedml.MultTableSEDMLWrapper
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
getInitialValues() - Method in class org.simulator.sbml.EquationSystem: Returns the initial values of the model to be simulated.
getInstance() - Static method in class fern.tools.Stochastics: Singleton pattern method.
getIntegerSolution() - Method in class org.simulator.fba.NewGLPKSolver
getIntegrator() - Method in class org.simulator.math.odes.FirstOrderSolver
getKey(int) - Method in class fern.simulation.algorithm.IndexedPriorityQueue: Gets the tau of a reaction by lookup in the index
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
getKiSAOterm() - Method in class org.simulator.math.odes.AdamsBashforthSolver
getKiSAOterm() - Method in class org.simulator.math.odes.AdamsMoultonSolver
getKiSAOterm() - Method in interface org.simulator.math.odes.DESSolver: For details about the Kinetic Simulation Algorithm Ontology (KiSAO) see http://biomodels.net/kisao/.
getKiSAOterm() - Method in class org.simulator.math.odes.DormandPrince54Solver
getKiSAOterm() - Method in class org.simulator.math.odes.DormandPrince853Solver
getKiSAOterm() - Method in class org.simulator.math.odes.EulerMethod
getKiSAOterm() - Method in class org.simulator.math.odes.GraggBulirschStoerSolver
getKiSAOterm() - Method in class org.simulator.math.odes.HighamHall54Solver
getKiSAOterm() - Method in class org.simulator.math.odes.RosenbrockSolver
getKiSAOterm() - Method in class org.simulator.math.odes.RungeKutta_EventSolver
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.
getLastTimeExecuted() - Method in class org.simulator.math.odes.EventInProgress: Returns the last time the event has been executed.
getLastTimeFired() - Method in class org.simulator.math.odes.EventInProgress: Returns the last time the event has been fired.
getLibraryNames() - Method in class org.simulator.fba.NewGLPKSolver
getMappings() - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getMath() - Method in class org.simulator.sbml.astnode.AssignmentRuleValue
getMathTree(int) - Method in class fern.network.sbml.SBMLPropensityCalculator: Gets the internal representation of the sbml kinetic law.
getMaxAbsDistances(MultiTable, MultiTable) - Method in class org.simulator.math.QualityMeasure
getMeanFunction() - Method in class org.simulator.math.QualityMeasure
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.
getModel() - Method in class org.simulator.sbml.EquationSystem: Returns the model that is used by this object.
getModelXMLFor(URI) - Method in class org.simulator.sedml.FileModelResolver: Makes a best effort to read an XML based model and return it as a String based upon the URI.
getMonomerAmount() - Method in class fern.network.creation.AutocatalyticNetwork: Gets the initial amount of the monomers for a simulation algorithm.
getMultiTable() - Method in class org.simulator.sedml.MultTableSEDMLWrapper: Gets the underlying MultiTable wrapped by this class.
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.
getName() - Method in class org.simulator.fba.NewGLPKSolver
getName() - Method in class org.simulator.math.odes.AbstractDESSolver: This gives a human-readable name of this solver that can be displayed in a graphical user interface.
getName() - Method in class org.simulator.math.odes.AdamsBashforthSolver
getName() - Method in class org.simulator.math.odes.AdamsMoultonSolver
getName() - Method in class org.simulator.math.odes.DormandPrince54Solver
getName() - Method in class org.simulator.math.odes.DormandPrince853Solver
getName() - Method in class org.simulator.math.odes.EulerMethod
getName() - Method in class org.simulator.math.odes.GraggBulirschStoerSolver
getName() - Method in class org.simulator.math.odes.HighamHall54Solver
getName() - Method in class org.simulator.math.odes.MultiTable.Block.Column
getName() - Method in class org.simulator.math.odes.MultiTable.Block
getName() - Method in class org.simulator.math.odes.MultiTable: Gives this MultiTable's name.
getName() - Method in class org.simulator.math.odes.RosenbrockSolver
getName() - Method in class org.simulator.math.odes.RungeKutta_EventSolver
getName() - Method in class org.simulator.sbml.astnode.ASTNodeValue: Returns the name of the corresponding ASTNode.
getNames() - Method in class fern.tools.Stochastics: Gets the names of the built-in distributions.
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.
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 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
getNextEventAssignments(double, double, double[]) - Method in interface org.simulator.math.odes.EventDESystem: Returns a list with event assignments for the events triggered either by the time t or by the concentrations of the species stored in Y.
getNextEventAssignments(double, double, double[]) - Method in class org.simulator.sbml.SBMLinterpreter: Returns a list with event assignments for the events triggered either by the time t or by the concentrations of the species stored in Y.
getNextThetaEvent() - Method in class fern.simulation.Simulator: Theta defines a moment, where the simulator has to invoke theta of a observer.
getNode() - Method in class org.simulator.sbml.astnode.ASTNodeValue
getNodeObject() - Method in class org.simulator.sbml.astnode.RuleValue
getNoDerivatives() - Method in interface org.simulator.math.odes.EventDESystem
getNoDerivatives() - Method in class org.simulator.sbml.EquationSystem
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.
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.
getNumBlocks() - Method in class org.simulator.math.odes.MultiTable
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
getNumColumns() - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getNumDataRows() - Method in class org.simulator.sedml.MultTableSEDMLWrapper
getNumEquations() - Method in class org.simulator.math.odes.RosenbrockSolver
getNumEventAssignments() - Method in class org.simulator.sbml.SBMLEventInProgress
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.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
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
getObjectiveValue() - Method in class org.simulator.fba.FluxBalanceAnalysis: Returns the objective value of the current solution.
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.
getParameterCount() - Method in interface org.simulator.math.odes.ParameterizedDESystem: Gives the number of parameters in the ParameterizedDESystem.
getParameterCount() - Method in class org.simulator.sbml.EquationSystem: This method tells you the complete number of parameters within the model.
getParameterIdentifiers() - Method in interface org.simulator.math.odes.ParameterizedDESystem: It is assumed that each parameter value in the system is associated with a unique identifier, which can be used to address it in numerical calculations.
getParameterValues() - Method in interface org.simulator.math.odes.ParameterizedDESystem: This method allows you to access all current values of the parameters within the ParameterizedDESystem in form of a double array.
getParentNetwork() - Method in class fern.network.modification.ModifierNetwork: Gets the parent network.
getPersistent() - Method in class org.simulator.sbml.SBMLEventInProgress
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.
getPositionOfParameters() - Method in class org.simulator.sbml.EquationSystem
getPositiveValueCount() - Method in interface org.simulator.math.odes.DESystem
getPositiveValueCount() - Method in class org.simulator.sbml.EquationSystem
getPrintWriter() - Method in class fern.simulation.observer.Observer: Gets the registered PrintWriter
getPriority() - Method in class org.simulator.sbml.SBMLEventInProgress: Return the priority of the associated event.
getPriorityObject() - Method in class org.simulator.sbml.SBMLEventInProgress
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
getProcessedResult() - Method in class org.simulator.sedml.ProcessSedMLResults
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.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.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.
getRateRulesRoots() - Method in class org.simulator.sbml.EquationSystem
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.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 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 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
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.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
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
getRelTol() - Method in class org.simulator.math.odes.AdaptiveStepsizeIntegrator
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 org.simulator.math.N_Metric: Returns the n of the metric.
getRow(int) - Method in class org.simulator.math.odes.MultiTable.Block: Delivers the given row of the data matrix as an array of doubles only, i.e., no time points.
getRowCount() - Method in class org.simulator.math.odes.MultiTable.Block.Column: Gives the number of rows in this MultiTable.Block.Column.
getRowCount() - Method in class org.simulator.math.odes.MultiTable.Block
getRowCount() - Method in class org.simulator.math.odes.MultiTable
getRuleCount() - Method in interface org.simulator.math.odes.EventDESystem: Counts the number of rules to be evaluated in each time point.
getRuleCount() - Method in class org.simulator.sbml.EquationSystem: Counts the number of rules to be evaluated in each time point.
getRuleObjects() - Method in class org.simulator.sbml.SBMLEventInProgress
getSbmlInterpreter() - Method in class fern.network.sbml.SBMLNetwork
getSBMLModel() - Method in class fern.network.sbml.SBMLNetwork: Gets the SBML model.
getSEDMLDescription() - Method in class org.simulator.omex.OMEXArchive
getSeed() - Method in class fern.tools.Stochastics: Gets the actual seed of the random number generator.
getSerialversionuid() - Static method in class org.simulator.math.odes.AbstractDESSolver
getSerialversionuid() - Static method in class org.simulator.math.odes.MultiTable
getShowSteps() - Method in class fern.benchmark.SimulatorPerformance: Gets the number of iterations between two present-calls.
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.
getSolution() - Method in class org.simulator.fba.FluxBalanceAnalysis: Returns solution values as a HashMap with key as reaction Id and value as the flux.
getSource() - Method in class org.simulator.sbml.ConstraintEvent
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 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 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.
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
getSpeciesReferenceID() - Method in class org.simulator.sbml.astnode.AssignmentRuleValue: Returns the id of the species reference (if present), null otherwise.
getSpectrum(float, Color...) - Static method in class fern.tools.ColorSpectrum: Gets a color representing the given number in an given color scale.
getStepSize() - Method in class org.simulator.math.odes.AbstractDESSolver
getStepSize() - Method in interface org.simulator.math.odes.DESSolver: Obtain the currently set integration step size.
getStoichiometry() - Method in class org.simulator.sbml.astnode.StoichiometryValue
getStoichiometrySet() - Method in class org.simulator.sbml.astnode.StoichiometryValue
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
getSymbolHash() - Method in class org.simulator.sbml.EquationSystem
getTheta() - Method in class fern.simulation.observer.Observer: Gets the moment in time, where the simulator has to invoke Observer.theta(double).
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.
getTime() - Method in class org.simulator.math.odes.EventInProgress: Return the next time of execution of the associated event.
getTime() - Method in class org.simulator.sbml.astnode.ASTNodeValue
getTime() - Method in class org.simulator.sbml.ConstraintEvent
getTimeconstraint() - Method in class org.simulator.fba.NewGLPKSolver
getTimeName() - Method in class org.simulator.math.odes.MultiTable: The column identifier for the first column, i.e., the time column.
getTimePoint(int) - Method in class org.simulator.math.odes.MultiTable: Returns the time value at the given index position.
getTimePoints() - Method in class org.simulator.math.odes.MultiTable.Block: Access to the time points of the overall table.
getTimePoints() - Method in class org.simulator.math.odes.MultiTable
getTriggerObject() - Method in class org.simulator.sbml.SBMLEventInProgress
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 tau < useSimpleFactor / a_0).
getUseValuesFromTriggerTime() - Method in class org.simulator.sbml.SBMLEventInProgress: Returns true if the values of the assignments are calculated at the trigger time of the event, otherwise false.
getValue(String) - Method in class org.simulator.fba.FluxBalanceAnalysis: Returns the solution value for the Reaction variable with the given identifier.
getValue(int) - Method in class org.simulator.math.odes.MultiTable.Block.Column: Access to the given row in this column.
getValue(double) - Method in class org.simulator.sbml.astnode.ASTNodeValue: Returns the value as an object (double or boolean)
getValue() - Method in class org.simulator.sbml.astnode.RuleValue: Returns the value of the rule.
getValueAt(int, int) - Method in class org.simulator.math.odes.MultiTable.Block
getValueAt(int, int) - Method in class org.simulator.math.odes.MultiTable
getValues() - Method in class org.simulator.fba.FluxBalanceAnalysis: Returns solution values for an array of Reaction variables.
getValues() - Method in class org.simulator.math.odes.EventInProgress: Return the values used in the next execution of the associated event.
getVariable() - Method in class org.simulator.sbml.astnode.RateRuleValue
getVolume() - Method in class fern.simulation.Simulator: Gets the volume of the reaction network.
getX(int) - Method in class fern.tools.gnuplot.Axes
getY() - Method in class org.simulator.sbml.EquationSystem: Get state array.
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.
GraggBulirschStoerSolver - Class in org.simulator.math.odes: This class is a wrapper for the Gragg-Bulirsch-Stoer solver in the Apache Math Library.
GraggBulirschStoerSolver() - Constructor for class org.simulator.math.odes.GraggBulirschStoerSolver: default constructor
GraggBulirschStoerSolver(double) - Constructor for class org.simulator.math.odes.GraggBulirschStoerSolver
GraggBulirschStoerSolver(double, boolean) - Constructor for class org.simulator.math.odes.GraggBulirschStoerSolver
GraggBulirschStoerSolver(GraggBulirschStoerSolver) - Constructor for class org.simulator.math.odes.GraggBulirschStoerSolver: clone constructor
GroupContainer - Class in fern.simulation.algorithm
GroupContainer(Simulator) - Constructor for class fern.simulation.algorithm.GroupContainer
gt(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

H

hasExecutionTime() - Method in class org.simulator.math.odes.EventInProgress: Returns true if the event is supposed to be executed at some time.
hasMoreAssignments(double) - Method in class org.simulator.math.odes.EventInProgress: Checks if this event has still assignments to perform for the given point in time
HighamHall54Solver - Class in org.simulator.math.odes: This class is a wrapper for the Higham-Hall-54 solver in the Apache Math Library.
HighamHall54Solver() - Constructor for class org.simulator.math.odes.HighamHall54Solver: default constructor
HighamHall54Solver(double) - Constructor for class org.simulator.math.odes.HighamHall54Solver
HighamHall54Solver(double, boolean) - Constructor for class org.simulator.math.odes.HighamHall54Solver
HighamHall54Solver(HighamHall54Solver) - Constructor for class org.simulator.math.odes.HighamHall54Solver: clone constructor
HistogramDistanceTestSet - Class in fern.example: Encapsulate test sets for histogram distance calculations.
HistogramDistanceTestSet(Simulator, double, int, double, String) - Constructor for class fern.example.HistogramDistanceTestSet
hqr(double[][], double[], double[]) - Static method in class org.simulator.math.MatrixOperations: Finds all eigenvalues of an upper Hessenberg matrix a[1..n][1..n].
HybridMaximalTimeStep - Class in fern.simulation.algorithm: This is an modified version of Maximal Time Step Method by Puchalka and Kierzec.
HybridMaximalTimeStep(Network) - Constructor for class fern.simulation.algorithm.HybridMaximalTimeStep

I

implies(ASTNodeValue, ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
inBetweenSteps(double, double, double) - Method in class org.simulator.math.odes.AbstractDESSolver: Computes the number of necessary steps between two time steps.
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
init(boolean, double, double, double, Map<String, Boolean>) - Method in class org.simulator.sbml.EquationSystem: This method initializes the differential equation system for simulation.
init() - Method in class org.simulator.sbml.SBMLinterpreter: This method initializes the differential equation system for simulation.
init(boolean) - Method in class org.simulator.sbml.SBMLinterpreter: This method initializes the differential equation system for simulation.
init(boolean, double, double, double) - Method in class org.simulator.sbml.SBMLinterpreter: This method initializes the differential equation system for simulation.
init(boolean, double, double, double, Map<String, Boolean>) - Method in class org.simulator.sbml.SBMLinterpreter: This method initializes the differential equation system for simulation.
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
initializePropensities() - Method in class fern.simulation.Simulator: Initializes the propensities.
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
IntegerValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of an integer node.
IntegerValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.IntegerValue
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.
IntervalObserver(Simulator, double, int, String[]) - Constructor for class fern.simulation.observer.IntervalObserver
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.
isCellEditable(int, int) - Method in class org.simulator.math.odes.MultiTable
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
isIncludeIntermediates() - Method in class org.simulator.math.odes.AbstractDESSolver
isIncludeIntermediates() - Method in interface org.simulator.math.odes.DESSolver: If this method returns true, intermediate results that may originate from a RichDESystem are included into the MultiTable that contains the result of a numerical integration.
isInterpolateTheta() - Method in class fern.simulation.Simulator: Gets whether the amount values are returned interpolated for theta events.
isName() - Method in class org.simulator.sbml.astnode.ASTNodeValue: Returns true if the corresponding ASTNode is of type name.
isNonnegative() - Method in class org.simulator.math.odes.AbstractDESSolver
isPlotQuality() - Method in class fern.simulation.observer.IntervalObserver: Gets whether or not to plot quality data.
isSetData() - Method in class org.simulator.math.odes.MultiTable.Block: Checks whether or not a data matrix has been defined in this object
isSetTimePoints() - Method in class org.simulator.math.odes.MultiTable: Checks whether an array of time points has been set for this object.
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.
isUnstable() - Method in class org.simulator.math.odes.AbstractDESSolver
isUnstable() - Method in interface org.simulator.math.odes.DESSolver: Method to check whether the solution of the numerical integration procedure contains Double.NaN values.
isVerbose() - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping: Gets if each step is to print to stdout.
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.
iterator() - Method in class org.simulator.math.odes.MultiTable.Block.Column
iterator() - Method in class org.simulator.math.odes.MultiTable

J

join(String[], String) - Static method in class fern.tools.NumberTools: Joins the array with the given glue to one String.

K

KineticConstantPropensityCalculator - Interface in fern.network

L

LacYComplete - Class in fern.example: The LacZ/LacY model of procaryotic gene expression proposed by [1] is simulated.
LacYComplete() - Constructor for class fern.example.LacYComplete
LacYHistogramDistances - Class in fern.example: The LacZ/LacY model of procaryotic gene expression proposed by [1] is simulated.
LacYHistogramDistances() - Constructor for class fern.example.LacYHistogramDistances
LacZ - Class in fern.example: The LacZ/LacY model of procaryotic gene expression proposed by [1] is simulated.
LacZ() - Constructor for class fern.example.LacZ
lambdaBoolean(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
lambdaDouble(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
LeapObserver - Class in fern.simulation.observer: Observes the amount of given molecule species at each step.
LeapObserver(Simulator, String...) - Constructor for class fern.simulation.observer.LeapObserver: Creates the observer with a given simulator and given species
leq(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
ln(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
loadHistogram(File) - Static method in class fern.tools.NumberTools: Reads a previously saved histogram from a file.
loadNetwork(File) - Static method in class fern.tools.NetworkTools: Loads a network from file identifying the type (FernML/SBML).
LocalParameterValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to a LocalParameter.
LocalParameterValue(ASTNodeInterpreter, ASTNode, LocalParameter) - Constructor for class org.simulator.sbml.astnode.LocalParameterValue
log(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
log(ASTNodeValue, ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
logger - Static variable in class org.simulator.sbml.astnode.ASTNodeInterpreter: A logger.
logger - Static variable in class org.simulator.sbml.astnode.ASTNodeValue: A Logger for this class.
lt(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
lubksb(double[][], int[], double[]) - Static method in class org.simulator.math.MatrixOperations: Solves the set of n linear equations AX = B.
ludcmp(double[][], int[]) - Static method in class org.simulator.math.MatrixOperations: Given a matrix a[1..n][1..n], this routine replaces it by the LU decomposition of a rowwise permutation of itself. a and n are input. a is output,l arrand as in equation (2.3.14) above; indx[1..n] is an output vector that records the row permutation effected by the partial pivoting; d (return value) is output +/- 1 depending on whether the number of row interchanges was even or odd respectively.

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.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
main(String[]) - Static method in class org.simulator.About
main(String[]) - Static method in class org.simulator.examples.BiomodelsExample: * Input: directory with models (containing the biomodels), first model to be simulated, last model to be simulated,
main(String[]) - Static method in class org.simulator.examples.CompExample: Starts a simulation at the command line.
main(String[]) - Static method in class org.simulator.examples.ConstraintExample
main(String[]) - Static method in class org.simulator.examples.FBAExample: Simple test function that reads and solves an SBML file in a flux balance constraints framework.
main(String[]) - Static method in class org.simulator.examples.OMEXExample
main(String[]) - Static method in class org.simulator.examples.SEDMLExample
main(String[]) - Static method in class org.simulator.examples.SimulatorExample: Starts a simulation at the command line.
main(String[]) - Static method in class org.simulator.fba.NewGLPKSolver
main(String[]) - Static method in class org.testsuite.SBMLTestSuiteRunnerWrapper: The wrapper executes the simulation of a given SBML file and writes result to a specified CSV file.
ManhattanDistance - Class in org.simulator.math: Class for computation of the Manhattan distance of two vectors.
ManhattanDistance() - Constructor for class org.simulator.math.ManhattanDistance: Initializes a new distance object
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
Mathematics - Class in org.simulator.math: This class contains a collection of mathematical functions like the faculty, logarithms and several trigonometric functions.
Mathematics() - Constructor for class org.simulator.math.Mathematics
MathTree - Class in fern.network.sbml: Representation of am evaluation tree.
MathTree(SBMLinterpreter, ASTNode) - Constructor for class fern.network.sbml.MathTree: Creates a MathTree ASTNode.
MatrixException() - Constructor for exception org.simulator.math.MatrixOperations.MatrixException: Constructor for MatrixException
MatrixException(String) - Constructor for exception org.simulator.math.MatrixOperations.MatrixException: Constructor for MatrixException with message
MatrixOperations - Class in org.simulator.math: Class used to perform matrix operations, focusing on finding vector solutions to the vector equation F(x) = 0.
MatrixOperations() - Constructor for class org.simulator.math.MatrixOperations
MatrixOperations.MatrixException - Exception in org.simulator.math: This exception is thrown when errors in the computation of matrix-related solutions, their eigenvalues or eigenvectors.
max(Iterable<Integer>) - Static method in class fern.tools.NumberTools: Gets the maximal value within the given Iterable.
MaxAbsDistance - Class in org.simulator.math: An implementation of maxAbsDistance.
MaxAbsDistance() - Constructor for class org.simulator.math.MaxAbsDistance
MaxDivergenceTolerance - Class in org.simulator.math: An implementation of core comparison metric of the simulator's result with the pre-defined results.
MaxDivergenceTolerance(double, double) - Constructor for class org.simulator.math.MaxDivergenceTolerance: Default constructor.
maximum(ASTNodeValue[], double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
MeanFunction - Class in org.simulator.math: In this class functions for the computation of an overall distance based on the distance values determined for each column of a table are defined.
MeanFunction() - Constructor for class org.simulator.math.MeanFunction
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.
min(int, int, int) - Static method in class org.simulator.math.Mathematics: This just computes the minimum of three integer values.
minimum(ASTNodeValue[], double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
minus(ASTNodeValue[], int, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
MinusValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of a minus node.
MinusValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.MinusValue
MODEL_ID - Static variable in class org.simulator.sbml.AddMetaInfo: string constant for (Sub-)Model id
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.
MultiTable - Class in org.simulator.math.odes: This data structure contains the an array of sorted time points and a matrix organized in one column per quantity for which data (measurement or simulation) are gathered.
MultiTable() - Constructor for class org.simulator.math.odes.MultiTable: Constructs an empty MultiTable object.
MultiTable(double[], double[][], String[]) - Constructor for class org.simulator.math.odes.MultiTable: Constructs a data object for the given values.
MultiTable(double[], double[][], String[], String[]) - Constructor for class org.simulator.math.odes.MultiTable
MultiTable.Block - Class in org.simulator.math.odes: A MultiTable.Block is a data structure with a two-dimensional double array of actual data together with identifiers for each column.
MultiTable.Block.Column - Class in org.simulator.math.odes: A column of the MultiTable.Block matrix.
MultTableSEDMLWrapper - Class in org.simulator.sedml: This class adapts the native results to an interface that the SED-ML processor can use to post-process results.
MultTableSEDMLWrapper(MultiTable) - Constructor for class org.simulator.sedml.MultTableSEDMLWrapper

N

N_Metric - Class in org.simulator.math: An implementation of an n-metric.
N_Metric() - Constructor for class org.simulator.math.N_Metric: Constructs a new NMetric with a default root of two.
N_Metric(double) - Constructor for class org.simulator.math.N_Metric: Constructs a new NMetric with a customized root.
NamedValue - Class in org.simulator.sbml.astnode: This class computes and stores values of variables occurring in a function.
NamedValue(ASTNodeInterpreter, ASTNode, FunctionValue) - Constructor for class org.simulator.sbml.astnode.NamedValue
NAN - Static variable in class org.testsuite.SBMLTestSuiteRunnerWrapper
neq(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
Network - Interface in fern.network: The central interface of the whole framework.
NetworkLoader - Class in fern.network
NetworkLoader() - Constructor for class fern.network.NetworkLoader
NetworkSearchAction - Interface in fern.analysis: Implementing classes of NetworkSearchAction are able to control/watch searches in AnalysisBase.
NetworkSearchAction.NeighborType - Enum in fern.analysis: Defines different types of neighborhoods in a Network.
NetworkTools - Class in fern.tools: Contains various helper methods dealing with the Network interface.
NetworkTools() - Constructor for class fern.tools.NetworkTools
NewGLPKSolver - Class in org.simulator.fba: Class for solving the linear programs.
NewGLPKSolver() - Constructor for class org.simulator.fba.NewGLPKSolver
NodeChecker - Interface in fern.analysis: Implementing classes can be used for a NetworkSearchActions checkReaction, checkSpecies, if the information whether or not to visit the nodes is not accessible for the NetworkSearchAction.
NodeCheckerByAnnotation - Class in fern.analysis: An instance of NodeCheckerByAnnotation can be used to control a search in AnalysisBase by a NetworkSearchAction.
NodeCheckerByAnnotation(String, String) - Constructor for class fern.analysis.NodeCheckerByAnnotation: Creates the NodeChecker with the specified annotation field and value.
not(ASTNodeValue, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
NumberTools - Class in fern.tools: Contains some common methods to handle number related data structures.
NumberTools() - Constructor for class fern.tools.NumberTools

O

Observer - Class in fern.simulation.observer: Implementing classes are used to observe certain aspects of simulations.
Observer(Simulator) - Constructor for class fern.simulation.observer.Observer: Creates an observer dedicated to one simulator.
OMEXArchive - Class in org.simulator.omex
OMEXArchive(File) - Constructor for class org.simulator.omex.OMEXArchive
OMEXExample - Class in org.simulator.examples
OMEXExample() - Constructor for class org.simulator.examples.OMEXExample
or(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
OrController - Class in fern.simulation.controller: Implements a SimulationController composed of many SimulationController.
OrController(SimulationController...) - Constructor for class fern.simulation.controller.OrController
org.simulator - package org.simulator: This package simply contains a default main program to display very basic licensing terms and other information.
org.simulator.comp - package org.simulator.comp
org.simulator.examples - package org.simulator.examples
org.simulator.fba - package org.simulator.fba: This package contains an implementation of flux balance analysis for COBRA models.
org.simulator.io - package org.simulator.io: Import and export of files.
org.simulator.math - package org.simulator.math: Classes that contain several mathematical operations.
org.simulator.math.odes - package org.simulator.math.odes: The various solver classes that are all derived from AbstractDESSolver.
org.simulator.omex - package org.simulator.omex
org.simulator.plot - package org.simulator.plot
org.simulator.sbml - package org.simulator.sbml: Classes for storing and interpreting an SBML model.
org.simulator.sbml.astnode - package org.simulator.sbml.astnode: Classes for efficient numerical treatment of equations in form of abstract syntax trees.
org.simulator.sedml - package org.simulator.sedml: Classes for reading and executing SED-ML files.
org.testsuite - package org.testsuite
ORIG_ID - Static variable in class org.simulator.sbml.AddMetaInfo: string constant for SBase id of original model

P

paint(Graphics) - Method in class fern.tools.gnuplot.GnuPlot
ParameterizedDESystem - Interface in org.simulator.math.odes: This class defines a differential equation system that contains parameters whose values influence its behavior.
PartialDerivativePropensityCalculator - Interface in fern.network
Path(int[]) - Constructor for class fern.analysis.ShortestPath.Path: Creates a path from an array.
PearsonCorrelation - Class in org.simulator.math: Implementation of the Pearson correlation.
PearsonCorrelation() - Constructor for class org.simulator.math.PearsonCorrelation: Default constructor.
PearsonCorrelation(double) - Constructor for class org.simulator.math.PearsonCorrelation: Constructor, which allows setting the parameter value for default value.
performReaction(int, int) - Method in interface fern.network.AmountManager: Reflects a (multiple) firing of a reaction by adjusting the populations of the reactants and the products.
performReaction(int, int) - Method in class fern.network.ConstantAmountManager
performReaction(int, int) - Method in class fern.network.DefaultAmountManager: Reflects a (multiple) firing of a reaction by adjusting the populations of the reactants and the products.
performStep(SimulationController) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping: Performs a tau leaping step.
performStep(SimulationController) - Method in class fern.simulation.algorithm.CompositionRejection
performStep(SimulationController) - Method in class fern.simulation.algorithm.GibsonBruckSimulator
performStep(SimulationController) - Method in class fern.simulation.algorithm.GillespieEnhanced
performStep(SimulationController) - Method in class fern.simulation.algorithm.GillespieSimple
performStep(SimulationController) - Method in class fern.simulation.algorithm.HybridMaximalTimeStep
performStep(SimulationController) - Method in class fern.simulation.Simulator: Performs one simulation step.
piecewise(ASTNodeValue[], double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
plot() - Method in class fern.tools.gnuplot.GnuPlot: Calls gnuplot to plot the data.
PlotMultiTable - Class in org.simulator.plot: This class adds output data-plot support to SBSCL
PlotMultiTable(MultiTable, String) - Constructor for class org.simulator.plot.PlotMultiTable: Initializes the JFreeChart and dataSet for the chart using MultiTable
PlotMultiTable(MultiTable) - Constructor for class org.simulator.plot.PlotMultiTable: Initializes the JFreeChart and dataSet for the chart using MultiTable with a default title
PlotProcessedSedmlResults - Class in org.simulator.plot: This class adds output data-plot support to SBSCL
PlotProcessedSedmlResults(IProcessedSedMLSimulationResults, String) - Constructor for class org.simulator.plot.PlotProcessedSedmlResults: Initializes the JFreeChart and dataSet for the chart using IProcessedSedMLSimulationResults
PlotProcessedSedmlResults(IProcessedSedMLSimulationResults, List<Curve>, String) - Constructor for class org.simulator.plot.PlotProcessedSedmlResults
plus(ASTNodeValue[], int, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
PlusValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of a plus node.
PlusValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.PlusValue
postRun() - Method in class fern.simulation.Simulator: Finalizes a simulation, i.e. call it, when this simulation will not be continued.
pow(ASTNodeValue, ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
PowerValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of a power expression.
PowerValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.PowerValue
preRun() - Method in class fern.simulation.Simulator: Initializes this simulator for the first run (or a further run starting from time 0).
present() - Method in class fern.benchmark.SimulatorCorrectness: Gets called after some iterations of the method benchmark in the base class.
present() - Method in class fern.benchmark.SimulatorFireTypes: Present results of this benchmark is gnuplot and text to stdout.
present() - Method in class fern.benchmark.SimulatorRandomNumbers: Present results of this benchmark is gnuplot and text to stdout.
present() - Method in class fern.benchmark.SimulatorTime: Present results of this benchmark is gnuplot and text to stdout.
print() - Method in class fern.simulation.observer.Observer: Gets called after the finish call and prints the results of this observer if a PrintWriter is registered.
Probability - Interface in fern.tools.functions: Function delegate for conditional probabilities.
Probability.Constant - Class in fern.tools.functions: Implementation that yields a constant (and hence independent) probability.
Probability.ReactionProbability - Class in fern.tools.functions: Implementation for the reaction probability for the autocatalytic network creation.
process(Map<AbstractTask, List<IRawSedmlSimulationResults>>) - Method in class org.simulator.sedml.ProcessSedMLResults: This method modifies jlibsedml's process method to support dataGenerators for repeatedTasks.
processAssignmentRules(double, double[]) - Method in interface org.simulator.math.odes.EventDESystem: Calculates the changes or assignments that are defined by all rules in the system at the given simulation time point.
processAssignmentRules(double, double[]) - Method in class org.simulator.sbml.SBMLinterpreter: Calculates the changes or assignments that are defined by all rules in the system at the given simulation time point.
processEvents(EventDESystem, double, double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver: Processes sudden changes in the system due to events in the EDES
processEventsAndRules(boolean, DESystem, double, double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver: Function for processing the events and rules at a certain time step.
processInitialAssignments(double, double[]) - Method in class org.simulator.sbml.SBMLinterpreter: Processes the initial assignments
processRule(double[], double, boolean) - Method in class org.simulator.sbml.astnode.AssignmentRuleValue: Processes the rule and saves the new value of the corresponding variable in the Y vector if changeY is set to true.
processRule(double[], double[], double) - Method in class org.simulator.sbml.astnode.RateRuleValue: Processes the rule and saves the new value of the corresponding variable in the changeRate vector.
processRules(EventDESystem, double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver: Function for processing the rules at a certain time step.
processRules(double, double[], double[], boolean) - Method in class org.simulator.sbml.SBMLinterpreter: Processes the rules
processSatisfiedAgain(ConstraintEvent) - Method in interface org.simulator.sbml.ConstraintListener: Notify that the constraints are satisfied again after violation.
processSatisfiedAgain(ConstraintEvent) - Method in class org.simulator.sbml.SimpleConstraintListener: Notify that the constraints are satisfied again after violation.
ProcessSedMLResults - Class in org.simulator.sedml: Processes raw simulation results according to instructions specified in the DataGenerator elements specified in the output.
ProcessSedMLResults(SedML, Output) - Constructor for class org.simulator.sedml.ProcessSedMLResults
processSimulationResults(Output, Map<AbstractTask, List<IRawSedmlSimulationResults>>) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor: Process raw data from simulations and return a output MultiTable which contains wanted Output
processViolation(ConstraintEvent) - Method in interface org.simulator.sbml.ConstraintListener: Processes the given ConstraintEvent.
processViolation(ConstraintEvent) - Method in class org.simulator.sbml.SimpleConstraintListener: Processes the given ConstraintEvent.
PROGRESS - Static variable in class org.simulator.math.odes.AbstractDESSolver: Key used when informing listeners about progress by this solver.
PropensityCalculator - Interface in fern.network: A PropensityCalculator is the way, a Network tells a Simulator how to calculate propensities for the reactions.
propensityChanged(int, double, double) - Method in class fern.simulation.algorithm.GroupContainer
propertyChange(PropertyChangeEvent) - Method in class org.simulator.examples.SimulatorExample
propertyChange(PropertyChangeEvent) - Method in class org.simulator.sbml.EquationSystem
putOrigId(SBMLDocument) - Static method in class org.simulator.sbml.AddMetaInfo: A static method which add id information of each element to userObjects map which is an element of AbstractTreeNode SBML class to store extra information
PWR - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants used to adapt the stepsize according to the error in the last step (see rodas.f)

Q

QualityMeasure - Class in org.simulator.math: This class is the basis of various implementations of distance functions.
QualityMeasure() - Constructor for class org.simulator.math.QualityMeasure: Default constructor.
QualityMeasure(double) - Constructor for class org.simulator.math.QualityMeasure: Constructor, which allows setting the parameter value for default value.
QualityMeasure(double, MeanFunction) - Constructor for class org.simulator.math.QualityMeasure: Constructor, which allows setting the parameter values for QualityMeasure.meanFunction and QualityMeasure.defaultValue.
quotient(ASTNodeValue, ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

R

RandomNumber - Class in fern.benchmark: Benchmarking of the time needed for different random number generations.
RandomNumber() - Constructor for class fern.benchmark.RandomNumber
RandomNumberGeneratorCallObserver - Class in fern.simulation.observer: Observes the calls to the random number generator and count the number of drawn random number of different distributions.
RandomNumberGeneratorCallObserver(Simulator) - Constructor for class fern.simulation.observer.RandomNumberGeneratorCallObserver: Creates the observer for the given simulator.
rateOf(EquationSystem, CallableSBase, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
RateRuleValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of a rate rule together with the variable of the rule.
RateRuleValue(ASTNodeValue, int, String) - Constructor for class org.simulator.sbml.astnode.RateRuleValue
RateRuleValue(ASTNodeValue, int, Species, int, boolean, SBMLValueHolder, String, boolean) - Constructor for class org.simulator.sbml.astnode.RateRuleValue: Constructor for a rule with a species as variable
RateRuleValue(ASTNodeValue, int, List<Integer>, SBMLValueHolder, String) - Constructor for class org.simulator.sbml.astnode.RateRuleValue: Constructor for a rule with a compartment as variable
reactionDiscovered(int) - Method in interface fern.analysis.NetworkSearchAction: Gets called when a reaction is inserted into the search structure.
reactionFinished(int) - Method in interface fern.analysis.NetworkSearchAction: Gets called when a reaction gets out of the search structure.
ReactionIntervalObserver - Class in fern.simulation.observer: Observes number of firings of reactions repeatedly after certain intervals.
ReactionIntervalObserver(Simulator, double, String...) - Constructor for class fern.simulation.observer.ReactionIntervalObserver: Creates the observer for a given simulator, a given interval and given neighbors.
ReactionIntervalObserver(Simulator, double, int...) - Constructor for class fern.simulation.observer.ReactionIntervalObserver: Creates the observer for a given simulator, a given interval and given reaction indices.
ReactionProbability(double, int) - Constructor for class fern.tools.functions.Probability.ReactionProbability
ReactionValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to a Reaction.
ReactionValue(ASTNodeInterpreter, ASTNode, Reaction) - Constructor for class org.simulator.sbml.astnode.ReactionValue
readMultiTableFromCSV(Model, String) - Method in class org.simulator.io.CSVImporter: Converts the content of the CSV file in the form of the MultiTable.
readNetwork(File) - Static method in class fern.network.NetworkLoader: Tries to read the given file and returns the network in it (if there is one)
recovered(double) - Method in class org.simulator.math.odes.EventInProgress: The trigger of the associated event has made a transition from true to false, so the event can be triggered again.
refresh(boolean) - Method in class org.simulator.math.odes.EventInProgress
refresh(double) - Method in class org.simulator.math.odes.EventInProgress: Refreshes the status of the event regarding the current time.
refresh() - Method in class org.simulator.sbml.astnode.StoichiometryValue: Refreshes the stoichiometry.
refresh(boolean) - Method in class org.simulator.sbml.SBMLEventInProgress
refresh(boolean) - Method in class org.simulator.sbml.SBMLEventInProgressWithDelay
refresh(double) - Method in class org.simulator.sbml.SBMLEventInProgressWithDelay
registerDelayValueHolder(DelayValueHolder) - Method in interface org.simulator.math.odes.DelayedDESystem
registerDelayValueHolder(DelayValueHolder) - Method in class org.simulator.sbml.EquationSystem
registerEvents(Simulator) - Method in class fern.network.sbml.SBMLNetwork: Registers the SBMLEventHandlerObserver for each event in the sbml file to the Simulator.
registerNewTheta(Observer, double) - Method in class fern.simulation.Simulator: Is called by Observer.setTheta(double).
reinitialize() - Method in class fern.simulation.algorithm.CompositionRejection
reinitialize() - Method in class fern.simulation.algorithm.GibsonBruckSimulator
reinitialize() - Method in class fern.simulation.algorithm.GillespieEnhanced
reinitialize() - Method in class fern.simulation.algorithm.GillespieSimple
reinitialize() - Method in class fern.simulation.algorithm.HybridMaximalTimeStep
reinitialize() - Method in class fern.simulation.Simulator: Reset propensities when a event has been executed.
RELATIVE - Static variable in class org.testsuite.SBMLTestSuiteRunnerWrapper
Relative_N_Metric - Class in org.simulator.math: Computes the relative distance of two vectors based on the N_Metric distance.
Relative_N_Metric() - Constructor for class org.simulator.math.Relative_N_Metric: Default constructor
Relative_N_Metric(double) - Constructor for class org.simulator.math.Relative_N_Metric: Initialization with a certain n
Relative_N_Metric(N_Metric) - Constructor for class org.simulator.math.Relative_N_Metric: Initialization with a given N_Metric
RelativeEuclideanDistance - Class in org.simulator.math: Class for computation of the relative Euclidean distance of two vectors.
RelativeEuclideanDistance() - Constructor for class org.simulator.math.RelativeEuclideanDistance: Initializes a new instance
RelativeManhattanDistance - Class in org.simulator.math: Class for computation of the relative Manhattan distance of two vectors.
RelativeManhattanDistance() - Constructor for class org.simulator.math.RelativeManhattanDistance: Initializes a new instance.
RelativeMaxDistance - Class in org.simulator.math: Computes the relative distance of two vectors based on the MaxAbsDistance distance.
RelativeMaxDistance() - Constructor for class org.simulator.math.RelativeMaxDistance: Default Constructor
RelativeMaxDistance(MaxAbsDistance) - Constructor for class org.simulator.math.RelativeMaxDistance: Initialization with a given MaxAbsDistance
RelativeSquaredError - Class in org.simulator.math: An implementation of the relative squared error with a default value to avoid division by zero.
RelativeSquaredError() - Constructor for class org.simulator.math.RelativeSquaredError: Constructs a new RelativeSquaredError.
RELMIN - Static variable in class org.simulator.math.odes.RosenbrockSolver: the minimum acceptable value of relTol - attempts to obtain higher accuracy than this are usually very expensive
remainder(ASTNodeValue, ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
removeBlock(int) - Method in class org.simulator.math.odes.MultiTable: Removes the MultiTable.Block with the given index from this data structure.
removeConstraintListener(ConstraintListener) - Method in class org.simulator.sbml.EquationSystem: Removes the given ConstraintListener from this interpreter.
removeConstraintListener(int) - Method in class org.simulator.sbml.EquationSystem: Removes the ConstraintListener with the given index from this interpreter.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.simulator.math.odes.AbstractDESSolver
removePropertyChangeListener(PropertyChangeListener) - Method in interface org.simulator.math.odes.DESSolver: remove PropertyChangedListener to this Solver
reset() - Method in class org.simulator.math.odes.AbstractDESSolver: Initialize with default integration step size and non-negative attribute true.
reset() - Method in class org.simulator.sbml.astnode.ASTNodeValue: Resets the node
resetAmount() - Method in interface fern.network.AmountManager: Resets the amount of each species to the initial amount retrieved by the networks AnnotationManager.
resetAmount() - Method in class fern.network.ConstantAmountManager
resetAmount() - Method in class fern.network.DefaultAmountManager: Resets the amount of each species to the initial amount retrieved by the networks AnnotationManager.
resetCounts() - Method in class fern.tools.Stochastics: Resets the counts for each distribution to zero.
resetSeed() - Method in class fern.tools.Stochastics: Sets the seed to the current date
resetState(double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver
RESULT - Static variable in class org.simulator.math.odes.AbstractDESSolver: Key used when informing listeners about change in the result by this solver.
REVERSIBLE_SUFFIX - Static variable in class fern.network.modification.ReversibleNetwork: Suffix which marks annotations for virtually created reverse reactions.
ReversibleNetwork - Class in fern.network.modification: Doubles each reaction in a way that each original unidirectional reaction becomes reversible.As proposed by ModifierNetwork, the reactions are not copied but the indices are redirected.
ReversibleNetwork(Network, PropensityCalculator) - Constructor for class fern.network.modification.ReversibleNetwork: Creates a new network from an original network and virtually creates for each reaction a new inverse reaction.
RichDESystem - Interface in org.simulator.math.odes: A RichDESystem is a DESystem that provides additional information besides the pure rate of change during its evaluation.
RND - Static variable in class fern.simulation.algorithm.IndexedPriorityQueue
rollback() - Method in interface fern.network.AmountManager: Restore the amount array from the recently saved one.
rollback() - Method in class fern.network.ConstantAmountManager
rollback() - Method in class fern.network.DefaultAmountManager: Restore the amount array from the recently saved one.
root(ASTNodeValue, ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
root(double, ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
RootFunctionValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to a root function.
RootFunctionValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.RootFunctionValue
RosenbrockSolver - Class in org.simulator.math.odes: An implementation of Rosenbrock's method to approximate ODE solutions.
RosenbrockSolver() - Constructor for class org.simulator.math.odes.RosenbrockSolver: default constructor
RosenbrockSolver(int, double) - Constructor for class org.simulator.math.odes.RosenbrockSolver
RosenbrockSolver(RosenbrockSolver) - Constructor for class org.simulator.math.odes.RosenbrockSolver: clone constructor
RuleValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of a rule together with the variable of the rule.
RuleValue(ASTNodeValue, int) - Constructor for class org.simulator.sbml.astnode.RuleValue
RuleValue(ASTNodeValue, int, Species, int, boolean, SBMLValueHolder, boolean) - Constructor for class org.simulator.sbml.astnode.RuleValue: Constructor for rules that refer to a species.
run(SimulationController) - Method in class fern.simulation.Simulator: Runs a simulation, after it's initialized by calling Simulator.preRun() (allows to continue a simulation).
run() - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor: This method is a wrapper to the runSimulations method from AbstractSedmlExecutor to add additional support for repeatedTasks.
RungeKutta_EventSolver - Class in org.simulator.math.odes: Runge-Kutta method.
RungeKutta_EventSolver() - Constructor for class org.simulator.math.odes.RungeKutta_EventSolver: default constructor
RungeKutta_EventSolver(double) - Constructor for class org.simulator.math.odes.RungeKutta_EventSolver
RungeKutta_EventSolver(double, boolean) - Constructor for class org.simulator.math.odes.RungeKutta_EventSolver
RungeKutta_EventSolver(RungeKutta_EventSolver) - Constructor for class org.simulator.math.odes.RungeKutta_EventSolver: clone constructor

S

SAFETY - Static variable in class org.simulator.math.odes.RosenbrockSolver: Constants used to adapt the stepsize according to the error in the last step (see rodas.f)
save() - Method in interface fern.network.AmountManager: Makes a copy of the amount array.
save() - Method in class fern.network.ConstantAmountManager
save() - Method in class fern.network.DefaultAmountManager: Makes a copy of the amount array.
saveData(File) - Method in class fern.tools.gnuplot.GnuPlot: Saves the gnuplot data to one ore more files.
saveExperimentToSEDML(double, double, double, AbstractDESSolver, Model, URI, OutputStream) - Method in class org.simulator.sedml.SEDMLWriter: Given a configured simulation, will write to SED-ML using the specified OutputStream.
saveHistogram(Map<Integer, Integer>, File) - Static method in class fern.tools.NumberTools: Writes a histogram to a file.
saveImage(File) - Method in class fern.tools.gnuplot.GnuPlot: Saves the plotted data to a png file.
savePlot(String, String) - Method in class org.simulator.plot.PlotProcessedSedmlResults: Helper function that can save the generated plot (simulationPath sedml file) as a PNG image with fileName in the results folder
saveToFile(File) - Method in class fern.network.fernml.FernMLNetwork: Saves the actual FernMLNetwork to a file.
saveToFile(File) - Method in class fern.network.sbml.SBMLNetwork: Saves the current SBMLNetwork to a file.
saveToFile(File, int, int) - Method in class fern.network.sbml.SBMLNetwork: Saves the current SBMLNetwork to a sbml file with given level and version.
SBMLEventHandlerObserver - Class in fern.network.sbml: Observer which handles an event of a sbml model.
SBMLEventHandlerObserver(Simulator, SBMLNetwork, SBMLinterpreter, Event) - Constructor for class fern.network.sbml.SBMLEventHandlerObserver: Creates the observer.
SBMLEventInProgress - Class in org.simulator.sbml: This class represents a compilation of all information calculated during simulation concerning events in SBML.
SBMLEventInProgress(boolean) - Constructor for class org.simulator.sbml.SBMLEventInProgress: Creates a new EventInProcess with the given boolean value indicating whether or not it can fire at the initial time point.
SBMLEventInProgressWithDelay - Class in org.simulator.sbml: This class represents a compilation of all information calculated during simulation concerning events in SBML.
SBMLEventInProgressWithDelay(boolean) - Constructor for class org.simulator.sbml.SBMLEventInProgressWithDelay: Creates a new SBMLEventInProcessWithDelay with the given boolean value indicating whether or not it can fire at time point 0d.
SBMLinterpreter - Class in org.simulator.sbml: This differential equation system (DESystem) takes a model in SBML format and maps it to a data structure that is understood by the AbstractDESSolver.
SBMLinterpreter(Model) - Constructor for class org.simulator.sbml.SBMLinterpreter: This constructs a new DESystem for the given SBML Model.
SBMLinterpreter(Model, double, double, double) - Constructor for class org.simulator.sbml.SBMLinterpreter
SBMLinterpreter(Model, double, double, double, Map<String, Boolean>) - Constructor for class org.simulator.sbml.SBMLinterpreter: Creates a new SBMLinterpreter
SBMLMathTreeTest - Class in fern.example
SBMLMathTreeTest() - Constructor for class fern.example.SBMLMathTreeTest
SBMLNetwork - Class in fern.network.sbml: For specifications of the sbml format refer to http:\\www.sbml.org.
SBMLNetwork(File) - Constructor for class fern.network.sbml.SBMLNetwork: Creates a network from a sbmlfile.
SBMLNetwork(File, boolean) - Constructor for class fern.network.sbml.SBMLNetwork: Creates a network from a sbml file.
SBMLPropensityCalculator - Class in fern.network.sbml: Propensity calculator which is used for SBMLNetworks.
SBMLPropensityCalculator(SBMLinterpreter) - Constructor for class fern.network.sbml.SBMLPropensityCalculator: Creates the MathTrees and parses the parameters.
SBMLTestSuiteRunnerWrapper - Class in org.testsuite: Wrapper for the SBML Test Suite The SBML Test Suite is a conformance testing system.
SBMLTestSuiteRunnerWrapper() - Constructor for class org.testsuite.SBMLTestSuiteRunnerWrapper
SBMLValueHolder - Interface in org.simulator.sbml: A SBMLValueHolder is necessary to provide the current values for Compartments, Species, Parameters, and SpeciesReferences at simulation time.
scale(double, double[]) - Static method in class org.simulator.math.Mathematics: Scales a vector with the given scalar.
search(IntSearchStructure, int[], int[], NetworkSearchAction) - Method in class fern.analysis.AnalysisBase: Performs a search starting at the given sources (which means the contents of speciesSource and reactionSource are the initial content of the search structure IntSearchStructure.
sec(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
sech(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
SEDMLExample - Class in org.simulator.examples: This test class shows how a SED-ML file can be interpreted and executed using SBML Simulator Core solvers.
SEDMLExample() - Constructor for class org.simulator.examples.SEDMLExample
SedMLSBMLSimulatorExecutor - Class in org.simulator.sedml: This class extends an abstract class from jlibsedml, which provides various support functions such as retrieving models, applying changes to models, working out what tasks need to be executed to achieve an Output, and post-processing of results.
SedMLSBMLSimulatorExecutor(SedML, Output, String) - Constructor for class org.simulator.sedml.SedMLSBMLSimulatorExecutor
SedMLSBMLSimulatorExecutor(SedML, Output, Map<String, Boolean>, String) - Constructor for class org.simulator.sedml.SedMLSBMLSimulatorExecutor
SEDMLWriter - Class in org.simulator.sedml: Writes a simulation configuration to SED-ML for export and sharing.
SEDMLWriter() - Constructor for class org.simulator.sedml.SEDMLWriter
setAbsTol(double) - Method in class org.simulator.math.odes.AdaptiveStepsizeIntegrator
setAmount(int, long) - Method in interface fern.network.AmountManager: Sets the current amount of a species.
setAmount(int, long) - Method in class fern.network.ConstantAmountManager
setAmount(int, long) - Method in class fern.network.DefaultAmountManager: Sets the current amount of a species.
setAmount(int, long) - Method in class fern.simulation.algorithm.GibsonBruckSimulator
setAmount(int, long) - Method in class fern.simulation.algorithm.GillespieEnhanced
setAmount(int, long) - Method in class fern.simulation.algorithm.HybridMaximalTimeStep
setAmount(int, long) - Method in class fern.simulation.Simulator: Sets the amount of the given species.
setCatalyzedKineticConstant(double) - Method in class fern.network.creation.AutocatalyticNetwork: Sets the kinetic constant for catalyzed reactions.
setColumnNames(String[]) - Method in class org.simulator.math.odes.MultiTable.Block
setComment(String) - Method in class org.simulator.sedml.SEDMLWriter: Set an optional human-readable comment to be added to the SED-ML file.
setCompartmentRateRule(RateRuleValue) - Method in class org.simulator.sbml.astnode.RateRuleValue
setConstant(int, double) - Method in class fern.network.ArrayKineticConstantPropensityCalculator
setCountGenerations(boolean) - Method in class fern.tools.Stochastics: Sets whether or not to count the number of random number generations
setCurrentTime(double) - Method in class org.simulator.sbml.EquationSystem
setData(double[][]) - Method in class org.simulator.math.odes.MultiTable.Block
setDefaultStyle(String) - Method in class fern.tools.gnuplot.GnuPlot: The defaultStyle is used, when no style is defined for an column in an axes object.
setDefaultValue(double) - Method in class org.simulator.math.QualityMeasure: Set the value to be returned by the distance function in cases, in which no distance can be computed.
setDefaultValue(double) - Method in class org.simulator.math.Relative_N_Metric
setDelayObject(ASTNodeValue) - Method in class org.simulator.sbml.SBMLEventInProgress: Sets the math of the delay to a specific ASTNodeObject.
setDelaysIncluded(boolean) - Method in interface org.simulator.math.odes.DESystem
setDelaysIncluded(boolean) - Method in class org.simulator.sbml.EquationSystem
setEfficientlyAdaptSum(boolean) - Method in class fern.simulation.algorithm.GillespieEnhanced
setEpsilon(double) - 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.
setEpsilon(double) - Method in class org.simulator.fba.FluxBalanceAnalysis: Set the value of the EPSILON specific to a particular FBC instance
setFastProcessComputation(boolean) - Method in interface org.simulator.math.odes.FastProcessDESystem
setFastProcessComputation(boolean) - Method in class org.simulator.sbml.EquationSystem
setIdentifiers(String[]) - Method in class org.simulator.math.odes.MultiTable.Block
setIncludeIntermediates(boolean) - Method in class org.simulator.math.odes.AbstractDESSolver
setIncludeIntermediates(boolean) - Method in interface org.simulator.math.odes.DESSolver: Allows switching whether or not intermediate results should be included into the MultiTable of the result.
setInitialAmount(int, long) - Method in class fern.network.creation.AutocatalyticNetwork
setInitialAmount(int, long) - Method in class fern.network.fernml.FernMLNetwork
setInitialAmount(int, long) - Method in class fern.network.modification.ExtractSubNetwork
setInitialAmount(int, long) - Method in class fern.network.modification.ModifierNetwork
setInitialAmount(int, long) - Method in interface fern.network.Network: Sets the initial amount of the specified molecule species.
setInitialAmount(int, long) - Method in class fern.network.sbml.SBMLNetwork
setInterpolateTheta(boolean) - Method in class fern.simulation.Simulator: Sets whether the amount values are returned interpolated for theta events.
setIsArchive(ArchiveComponents) - Method in class org.simulator.sedml.SedMLSBMLSimulatorExecutor: Enables models to be retrieved from a SED-ML archive format.
setLabel(int, String) - Method in class fern.tools.gnuplot.Axes: Sets the label for a column.
setLabelFormat(String) - Method in class fern.simulation.observer.Observer: Sets the label format for Observer.getLabel(String).
setLangevinThreshold(double) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping: The Langevin threshold determines, when the normal distribution is used as an approximation for the poisson distribution.
setMath(ASTNode) - Method in class org.simulator.sbml.astnode.FunctionValue: Sets the math and evaluation block of the function definition.
setMeanFunction(MeanFunction) - Method in class org.simulator.math.QualityMeasure
setMonomerAmount(long) - Method in class fern.network.creation.AutocatalyticNetwork: Sets the initial amount of the monomers for a simulation algorithm.
setName(String) - Method in class org.simulator.math.odes.MultiTable.Block
setName(String) - Method in class org.simulator.math.odes.MultiTable: Sets the name of this MultiTable.
setNCritical(int) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping: The nCritical determines, when a reaction is called critical.
setNetworkAnnotation(String, String) - Method in interface fern.network.AnnotationManager: Sets the network annotation of the specified field.
setNetworkAnnotation(String, String) - Method in class fern.network.AnnotationManagerImpl
setNetworkAnnotation(String, String) - Method in class fern.network.fernml.FernMLAnnotationManager
setNonnegative(boolean) - Method in class org.simulator.math.odes.AbstractDESSolver
setNumBins(int) - Method in class fern.benchmark.Benchmark: Sets the number of bins that are used for creating gnuplot histograms.
setNumSimpleCalls(int) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping: The numSimpleCalls determines, how often the SSA is called, when tau leaping is abandoned.
setOtherAmount(long) - Method in class fern.network.creation.AutocatalyticNetwork: Sets the initial amount of the not-monomers for a simulation algorithm.
setParameters(double[]) - Method in interface org.simulator.math.odes.ParameterizedDESystem: With this method it is possible to change the values of particular parameters.
setParameters(double[]) - Method in class org.simulator.sbml.SBMLinterpreter: This method allows us to set the parameters of the model to the specified values in the given array.
setPersistent(boolean) - Method in class org.simulator.sbml.SBMLEventInProgress: Sets the persistent flag of the event.
setPlotQuality(boolean) - Method in class fern.simulation.observer.IntervalObserver: Sets whether or not to plot quality data.
setPreviousTimePoint(double) - Method in class org.simulator.sbml.EquationSystem
setPrintWriter(PrintWriter) - Method in class fern.simulation.observer.Observer: Registers a PrintWriter
setPriorityObject(ASTNodeValue) - Method in class org.simulator.sbml.SBMLEventInProgress: Sets the math of the priority to a specific ASTNodeObject.
setReactionAnnotation(int, String, String) - Method in interface fern.network.AnnotationManager: Sets the reaction annotation of the specified field.
setReactionAnnotation(int, String, String) - Method in class fern.network.AnnotationManagerImpl
setReactionAnnotation(int, String, String) - Method in class fern.network.fernml.FernMLAnnotationManager
setRecordStart(double) - Method in class fern.simulation.observer.ReactionIntervalObserver: Sets the moment in time where the recording starts
setRelTol(double) - Method in class org.simulator.math.odes.AdaptiveStepsizeIntegrator
setRoot(double) - Method in class org.simulator.math.EuclideanDistance
setRoot(double) - Method in class org.simulator.math.ManhattanDistance
setRoot(double) - Method in class org.simulator.math.N_Metric: Sets the root.
setRoot(double) - Method in class org.simulator.math.Relative_N_Metric: Sets the root
setRoot(double) - Method in class org.simulator.math.RelativeEuclideanDistance
setRoot(double) - Method in class org.simulator.math.RelativeManhattanDistance
setRowData(int, double[]) - Method in class org.simulator.math.odes.MultiTable.Block: Sets the given array as the new row in the given position of the data matrix, but requires that the number of values in the array equal the number of columns in the matrix.
setSeed(long) - Method in class fern.tools.Stochastics: Sets a new seed for the random number generator.
setSeed(Date) - Method in class fern.tools.Stochastics: Sets a new seed for the random number generator.
setShowSteps(int) - Method in class fern.benchmark.SimulatorPerformance: Sets the number of iterations between two present-calls.
setSimulatorAsync(Simulator) - Method in class fern.network.sbml.SBMLEventHandlerObserver
setSpeciesAnnotation(int, String, String) - Method in interface fern.network.AnnotationManager: Sets the species annotation of the specified field.
setSpeciesAnnotation(int, String, String) - Method in class fern.network.AnnotationManagerImpl
setSpeciesAnnotation(int, String, String) - Method in class fern.network.fernml.FernMLAnnotationManager
setStepSize(double) - Method in class org.simulator.math.odes.AbstractDESSolver
setStepSize(double) - Method in interface org.simulator.math.odes.DESSolver: Set the integration step size.
setStepSize(double) - Method in class org.simulator.math.odes.FirstOrderSolver
setStochasticSeed(long) - Method in class fern.simulation.Simulator: Sets the seed for a particular model.
setStyle(int, String) - Method in class fern.tools.gnuplot.Axes: Sets the style for a column.
setTheta(double) - Method in class fern.simulation.observer.Observer: Sets the moment in time, where the simulator has to invoke Observer.theta(double).
setThetaMethod(boolean) - 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.
setTime(double) - Method in class fern.simulation.controller.DefaultController: Sets the time where the simulation has to stop.
setTime(double) - Method in class org.simulator.sbml.astnode.ASTNodeValue
setTimeconstraint(int) - Method in class org.simulator.fba.NewGLPKSolver
setTimeName(String) - Method in class org.simulator.math.odes.MultiTable: Set the name of the time column
setTimePoints(double[]) - Method in class org.simulator.math.odes.MultiTable
setTriggerObject(ASTNodeValue) - Method in class org.simulator.sbml.SBMLEventInProgress: Sets the math of the trigger to a specific ASTNodeObject.
setUncatalyzedKineticConstant(double) - Method in class fern.network.creation.AutocatalyticNetwork: Sets the kinetic constant for not catalyzed reactions.
setUnstableFlag(boolean) - Method in class org.simulator.math.odes.AbstractDESSolver
setUseSimpleFactor(double) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping: The useSimpleFactor determines, when the tau leaping is abandoned and the SSA method is used (if tau < useSimpleFactor / a_0).The default value is 10.
setUseValuesFromTriggerTime(boolean) - Method in class org.simulator.sbml.SBMLEventInProgress: Sets the useValuesFromTriggerTime value of the event.
setValue(double, int) - Method in class org.simulator.math.odes.MultiTable.Block.Column: Change the entry at the given row in this MultiTable.Block.Column.
setValueAt(Object, int, int) - Method in class org.simulator.math.odes.MultiTable.Block
setValueAt(Double, int, int) - Method in class org.simulator.math.odes.MultiTable
setVerbose(boolean) - Method in class fern.simulation.algorithm.AbstractBaseTauLeaping: Sets if each step is to print to stdout.
setVolume(double) - Method in class fern.simulation.algorithm.GibsonBruckSimulator
setVolume(double) - Method in class fern.simulation.algorithm.GillespieEnhanced
setVolume(double) - Method in class fern.simulation.algorithm.HybridMaximalTimeStep
setVolume(double) - Method in class fern.simulation.Simulator: Sets the volume of the reaction network.
ShortestPath - Class in fern.analysis: Computes shortest paths in the network by a bfs.
ShortestPath(Network) - Constructor for class fern.analysis.ShortestPath: Creates the class with the specified network.
ShortestPath.Path - Class in fern.analysis: Encapsulates a path from one species to another.
shuffle(int[]) - Static method in class fern.tools.NumberTools: Shuffles the content of the given array.
sign(double, double) - Static method in class org.simulator.math.MatrixOperations: Returns the value of a or |a| with the same sign as b
SimpleConstraintListener - Class in org.simulator.sbml: This class represents a simple listener implementation to process the violation of Constraints during simulation by logging the violation event in form of a warning.
SimpleConstraintListener() - Constructor for class org.simulator.sbml.SimpleConstraintListener
SimulationController - Interface in fern.simulation.controller: Simulators are controlled by implementing classes.
Simulator - Class in fern.simulation: Base class for stochastic simulators.
Simulator(Network) - Constructor for class fern.simulation.Simulator: Creates a new simulator for the given network.
Simulator.FireType - Enum in fern.simulation: Defines different types of a firing for reactions.
SimulatorCorrectness - Class in fern.benchmark: Benchmark the correctness of the built-in simulators for a given net.
SimulatorCorrectness(Network, double, String...) - Constructor for class fern.benchmark.SimulatorCorrectness: Creates the benchmark instance with given network, moment in time and species.
SimulatorExample - Class in org.simulator.examples: A simple program that performs a simulation of a model.
SimulatorExample() - Constructor for class org.simulator.examples.SimulatorExample
SimulatorFireTypes - Class in fern.benchmark: Benchmark the Simulator.FireTypes for a given net.
SimulatorFireTypes(Network, double) - Constructor for class fern.benchmark.SimulatorFireTypes: Create the benchmark and defines the time each simulator has to run in one iteration.
SimulatorPerformance - Class in fern.benchmark: Measures the performance of the different simulation algorithms for a given network.
SimulatorPerformance(Network) - Constructor for class fern.benchmark.SimulatorPerformance: Registers the six built-in simulators for the performance benchmarks.
SimulatorRandomNumbers - Class in fern.benchmark: Check the number of random number creations of different distributions for a given net.
SimulatorRandomNumbers(Network, double) - Constructor for class fern.benchmark.SimulatorRandomNumbers: Create the benchmark and defines the time each simulator has to run in one iteration.
SimulatorTime - Class in fern.benchmark
SimulatorTime(Network, double) - Constructor for class fern.benchmark.SimulatorTime: Create the benchmark and defines the time each simulator has to run in one iteration.
sin(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
sinh(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
size() - Method in class fern.simulation.algorithm.IndexedPriorityQueue: Gets the number of nodes in the binary heap.
solve(double, double) - Method in class org.simulator.comp.CompSimulator: This method initializes the RosenbrockSolver and passes it to solve the flattened model.
solve(double, double, DESSolver) - Method in class org.simulator.comp.CompSimulator: This method computes the numerical solution of the flattened SBML Model simulated using the RosenbrockSolver and then maps the solutions from the flattened model back to the original model.
solve(File) - Method in class org.simulator.examples.FBAExample
solve() - Method in class org.simulator.fba.FluxBalanceAnalysis: Solves the linear program that is defined in the SBMLDocument with which this solver was initialized.
solve(LinearProgram) - Method in class org.simulator.fba.NewGLPKSolver
solve(DESystem, double[], double, double) - Method in class org.simulator.math.odes.AbstractDESSolver: Solves the given differential equation system
solve(DESystem, double[], double, double, PropertyChangeListener) - Method in class org.simulator.math.odes.AbstractDESSolver: Solves the given differential equation system
solve(DESystem, double[], double, double, int) - Method in class org.simulator.math.odes.AbstractDESSolver: Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.
solve(DESystem, double[], double, double, int, PropertyChangeListener) - Method in class org.simulator.math.odes.AbstractDESSolver: Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.
solve(DESystem, double[], double[]) - Method in class org.simulator.math.odes.AbstractDESSolver: Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.
solve(DESystem, double[], double[], PropertyChangeListener) - Method in class org.simulator.math.odes.AbstractDESSolver: Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.
solve(DESystem, MultiTable.Block, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver: Solves the given DESystem using new initial conditions in each time step.
solve(DESystem, MultiTable.Block, double[], PropertyChangeListener) - Method in class org.simulator.math.odes.AbstractDESSolver: Solves the given DESystem using new initial conditions in each time step.
solve(DESystem, double[], double, double, PropertyChangeListener) - Method in interface org.simulator.math.odes.DESSolver: Solves the given differential equation system
solve(DESystem, double[], double, double) - Method in interface org.simulator.math.odes.DESSolver: Solves the given differential equation system
solve(DESystem, double[], double, double, int, PropertyChangeListener) - Method in interface org.simulator.math.odes.DESSolver: Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.
solve(DESystem, double[], double, double, int) - Method in interface org.simulator.math.odes.DESSolver: Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.
solve(DESystem, double[], double[], PropertyChangeListener) - Method in interface org.simulator.math.odes.DESSolver: Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.
solve(DESystem, double[], double[]) - Method in interface org.simulator.math.odes.DESSolver: Solves the given differential equation system with the step size h and the number of steps as given starting at the value x.
solve(DESystem, MultiTable.Block, double[], PropertyChangeListener) - Method in interface org.simulator.math.odes.DESSolver: Solves the given DESystem using new initial conditions in each time step.
solve(DESystem, MultiTable.Block, double[]) - Method in interface org.simulator.math.odes.DESSolver: Solves the given DESystem using new initial conditions in each time step.
speciesDiscovered(int) - Method in interface fern.analysis.NetworkSearchAction: Gets called when a species is inserted into the search structure.
speciesFinished(int) - Method in interface fern.analysis.NetworkSearchAction: Gets called when a species gets out of the search structure.
SpeciesReferenceValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to a SpeciesReference.
SpeciesReferenceValue(ASTNodeInterpreter, ASTNode, SpeciesReference, SBMLValueHolder) - Constructor for class org.simulator.sbml.astnode.SpeciesReferenceValue
SpeciesValue - Class in org.simulator.sbml.astnode: This class computes and stores values of ASTNodes that refer to a Species.
SpeciesValue(ASTNodeInterpreter, ASTNode, Species, SBMLValueHolder, int, int, String, boolean, boolean) - Constructor for class org.simulator.sbml.astnode.SpeciesValue
sqrt(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
start() - Method in class fern.benchmark.Benchmark: sets a start time for the benchmark system
start(double) - Method in class fern.simulation.Simulator: Starts the simulation up to a given time.
start(SimulationController) - Method in class fern.simulation.Simulator: Start the simulation with the given SimulationController.
Start - Class in fern
Start() - Constructor for class fern.Start
started() - Method in class fern.example.CellGrowthObserver
started() - Method in class fern.network.sbml.SBMLEventHandlerObserver
started() - Method in class fern.simulation.observer.AmountAtMomentObserver: Register theta at the simulator.
started() - Method in class fern.simulation.observer.FireTypeObserver: Do nothing.
started() - Method in class fern.simulation.observer.InstantOutputObserver: Prints event.
started() - Method in class fern.simulation.observer.IntervalObserver: Clears the recorded values and registers (if needed) theta
started() - Method in class fern.simulation.observer.LeapObserver: Clears the recorded data.
started() - Method in class fern.simulation.observer.Observer: Gets called when the simulation has started after the initialization and before the termination condition is checked the first time.
started() - Method in class fern.simulation.observer.RandomNumberGeneratorCallObserver: Resets the count variables of the random number generator calls.
started() - Method in class fern.simulation.observer.ReactionIntervalObserver
stddev(double[]) - Static method in class fern.tools.NumberTools: Gets the standard deviation of the array
steadystate(DESystem, double[], double) - Method in class org.simulator.math.odes.AbstractDESSolver
step() - Method in class fern.example.CellGrowthObserver
step() - Method in class fern.network.sbml.SBMLEventHandlerObserver
step() - Method in class fern.simulation.observer.AmountAtMomentObserver: Do nothing.
step() - Method in class fern.simulation.observer.FireTypeObserver: Do nothing.
step() - Method in class fern.simulation.observer.InstantOutputObserver: Prints event.
step() - Method in class fern.simulation.observer.IntervalObserver: If the step method is used, the data is recorded here.
step() - Method in class fern.simulation.observer.LeapObserver: Record the time and amounts of the species.
step() - Method in class fern.simulation.observer.Observer: Gets called after each termination check and before Simulator.performStep(fern.simulation.controller.SimulationController) is called.
step() - Method in class fern.simulation.observer.RandomNumberGeneratorCallObserver: Do nothing.
step(DESystem) - Method in class org.simulator.math.odes.RosenbrockSolver: This function tries to make a time step.
STEPS - Static variable in class org.testsuite.SBMLTestSuiteRunnerWrapper
Stochastics - Class in fern.tools: Manages a random number generators for various distributions.
StoichiometryValue - Class in org.simulator.sbml.astnode: Computes for a SpeciesReference with a stoichiometry occuring in some Reaction the stoichiometry.
StoichiometryValue(SpeciesReference, int, Map<String, Double>, double[], ASTNodeValue) - Constructor for class org.simulator.sbml.astnode.StoichiometryValue
STPMX - Static variable in class org.simulator.math.MatrixOperations: Scaled maximum step length allowed in line searches
sum(int[]) - Static method in class fern.tools.NumberTools: Gets the sum of the values in the array.
svMult(double, double[], double[]) - Static method in class org.simulator.math.Mathematics: Multiplies (scales) every element of the array v with s in place.
svvAddAndScale(double, double[], double[], double[]) - Static method in class org.simulator.math.Mathematics: Add vectors scaled: res[i] = s*(v[i] + w[i])
svvAddScaled(double, double[], double[], double[]) - Static method in class org.simulator.math.Mathematics: Add vectors scaled: res[i] = s*v[i] + w[i]
swap(double, double) - Static method in class org.simulator.math.Mathematics: Swaps a and b if a is greater then b.
symbolTime() - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

T

tan(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
tanh(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
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
TEMP_VALUE - Static variable in class fern.network.sbml.MathTree
TEMP_VALUE - Static variable in class org.simulator.sbml.EquationSystem: Key to memorize user objects in ASTNode
testBiomodels(String, int, int) - Static method in class org.simulator.examples.BiomodelsExample: Tests the models of biomodels.org using the RosenbrockSolver as integrator
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
times(ASTNodeValue[], int, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
TimesValue - Class in org.simulator.sbml.astnode: This class can compute and store the value of times nodes.
TimesValue(ASTNodeInterpreter, ASTNode) - Constructor for class org.simulator.sbml.astnode.TimesValue: Initializes a new instance with the interpreter and ASTNode given
TINY - Static variable in class org.simulator.math.MatrixOperations: Extremely small value.
toDoubleArray(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.
toIntArray(Collection<Integer>) - Static method in class fern.tools.NumberTools: Copies the values of the given collection and unboxes them to an array.
TOLF - Static variable in class org.simulator.math.MatrixOperations: Convergence criterion on function values
TOLMIN - Static variable in class org.simulator.math.MatrixOperations: Criterion deciding whether spurious convergence to a minimum of min
TOLX - Static variable in class org.simulator.math.MatrixOperations: Convergence criterion on delta X
toString() - Method in class fern.analysis.ShortestPath.Path
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
toString() - Method in class org.simulator.math.odes.MultiTable.Block.Column
toString() - Method in class org.simulator.math.odes.MultiTable.Block
toString() - Method in class org.simulator.math.odes.MultiTable
toString(ASTNode) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
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

U

uMinus(ASTNodeValue, double, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter
unitRoundoff() - Method in class org.simulator.math.odes.RosenbrockSolver: Returns an approximation to the error involved with the current arithmetic implementation
update(int, double) - Method in class fern.simulation.algorithm.IndexedPriorityQueue: Updates the tau of a reaction to a given value
updateSpeciesConcentration(AmountManager) - Method in class org.simulator.sbml.SBMLinterpreter: Updates the species concentration as per the updated values in the AmountManager.
useActualAmountAsInitialAmount(Network) - Static method in class fern.tools.NetworkTools: Copies the actual amount of the species in the network to its initial amount.

V

valueOf(String) - Static method in enum fern.analysis.NetworkSearchAction.NeighborType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fern.simulation.Simulator.FireType: Returns the enum constant of this type with the specified name.
values() - Static method in enum fern.analysis.NetworkSearchAction.NeighborType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fern.simulation.Simulator.FireType: Returns an array containing the constants of this enum type, in the order they are declared.
vvAdd(double[], double[], double[]) - Static method in class org.simulator.math.Mathematics: Add vectors in place setting res = v1 + v2.
vvAddOffs(double[], int, double[], int, double[], int, int) - Static method in class org.simulator.math.Mathematics: Add vectors in place setting with an offset within the target vector, meaning that res[resOffs+i]=v1[v1Offs+i]+v2[v2Offs+i] for i in length.
vvSub(double[], double[]) - Static method in class org.simulator.math.Mathematics: Subtract vectors returning a new vector c = a - b.
vvSub(double[], double[], double[]) - Static method in class org.simulator.math.Mathematics: Subtract vectors returning a new vector c = a - b.

X

xor(ASTNodeValue[], double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreter

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