Uses of Interface
fern.network.Network

Packages that use Network

Package	Description
fern.analysis
fern.benchmark
fern.network
fern.network.creation
fern.network.fernml
fern.network.modification
fern.network.sbml
fern.simulation
fern.simulation.algorithm
fern.tools

Uses of Network in fern.analysis

Methods in fern.analysis with parameters of type Network

Modifier and Type	Method and Description
boolean	NodeCheckerByAnnotation.checkReactionNode(Network network, int reaction)
boolean	NodeChecker.checkReactionNode(Network network, int reaction)
boolean	NodeCheckerByAnnotation.checkSpeciesNode(Network network, int species)
boolean	NodeChecker.checkSpeciesNode(Network network, int species)
void	NetworkSearchAction.initialize(Network net) Gets called before anything is inserted into the search structure.

Constructors in fern.analysis with parameters of type Network

Constructor and Description
AnalysisBase(Network network) Creates an analysis instance.
AutocatalyticNetworkDetection(Network network) Creates the AutocatalyticDetection by using the in the network built in CatalystIterator.
AutocatalyticNetworkDetection(Network network, CatalystIterator cataIt) Creates the AutocatalyticDetection by using the second argument as CatalystIterator.
ShortestPath(Network network) Creates the class with the specified network.

Uses of Network in fern.benchmark

Constructors in fern.benchmark with parameters of type Network

Constructor and Description
SimulatorCorrectness(Network net, double moment, String... speciesNames) Creates the benchmark instance with given network, moment in time and species.
SimulatorFireTypes(Network net, double time) Create the benchmark and defines the time each simulator has to run in one iteration.
SimulatorPerformance(Network net) Registers the six built-in simulators for the performance benchmarks.
SimulatorRandomNumbers(Network net, double time) Create the benchmark and defines the time each simulator has to run in one iteration.
SimulatorTime(Network net, double time) Create the benchmark and defines the time each simulator has to run in one iteration.

Uses of Network in fern.network

Classes in fern.network that implement Network

Modifier and Type	Class and Description
class	AbstractNetworkImpl Base implementation for the Network interface.

Methods in fern.network that return Network

Modifier and Type	Method and Description
static Network	NetworkLoader.readNetwork(File file) Tries to read the given file and returns the network in it (if there is one)

Constructors in fern.network with parameters of type Network

Constructor and Description
DefaultAmountManager(Network net) Creates an AmountManager for a given network

Uses of Network in fern.network.creation

Classes in fern.network.creation that implement Network

Modifier and Type	Class and Description
class	AutocatalyticNetwork Evolve an autocatalytic network.

Uses of Network in fern.network.fernml

Classes in fern.network.fernml that implement Network

Modifier and Type	Class and Description
class	FernMLNetwork A FernMLNetwork is usually loaded from a file.

Constructors in fern.network.fernml with parameters of type Network

Constructor and Description
FernMLNetwork(Network net) Create a FernMLNetwork from an existing Network.
FernMLNetwork(Network net, double[] kineticConstants) 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.

Uses of Network in fern.network.modification

Classes in fern.network.modification that implement Network

Modifier and Type	Class and Description
class	CatalysedNetwork Modifies the network by adding reactions X+C → Y+C (where C is each catalyst of the original reaction).
class	ExtractSubNetwork Extracts some reactions / species from a given net to form a new network.
class	ModifierNetwork Base class for modified networks, which implements the full Network interface.
class	ReversibleNetwork 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.

Methods in fern.network.modification that return Network

Modifier and Type	Method and Description
Network	ModifierNetwork.getOriginalNetwork() Gets the original network.
Network	ModifierNetwork.getParentNetwork() Gets the parent network.

Constructors in fern.network.modification with parameters of type Network

Constructor and Description
CatalysedNetwork(Network originalNet) Create a catalyzed network from an original network.
ExtractSubNetwork(Network originalNet, cern.colt.bitvector.BitVector reactions, cern.colt.bitvector.BitVector species) Extracts a given subnet from a network.
ModifierNetwork(Network originalNet) Creates a ModifierNetwork from an original network.
ReversibleNetwork(Network originalNet, PropensityCalculator reversiblePropensityCalculator) Creates a new network from an original network and virtually creates for each reaction a new inverse reaction.

Uses of Network in fern.network.sbml

Classes in fern.network.sbml that implement Network

Modifier and Type	Class and Description
class	SBMLNetwork For specifications of the sbml format refer to http:\\www.sbml.org.

Uses of Network in fern.simulation

Methods in fern.simulation that return Network

Modifier and Type	Method and Description
Network	Simulator.getNet() Gets the simulation network.

Constructors in fern.simulation with parameters of type Network

Constructor and Description
Simulator(Network net) Creates a new simulator for the given network.

Uses of Network in fern.simulation.algorithm

Constructors in fern.simulation.algorithm with parameters of type Network

Constructor and Description
AbstractBaseTauLeaping(Network net) Create the simulator for a given network.
AbstractTauLeapingPropensityBoundSimulator(Network net)
CompositionRejection(Network net)
DependencyGraph(Network net) Creates the dependency graph for a given network
GibsonBruckSimulator(Network net)
GillespieEnhanced(Network net)
GillespieSimple(Network net)
HybridMaximalTimeStep(Network net)
TauLeapingAbsoluteBoundSimulator(Network net)
TauLeapingRelativeBoundSimulator(Network net)
TauLeapingSpeciesPopulationBoundSimulator(Network net)

Uses of Network in fern.tools

Methods in fern.tools that return Network

Modifier and Type	Method and Description
static Network	NetworkTools.loadNetwork(File file) Loads a network from file identifying the type (FernML/SBML).

Methods in fern.tools with parameters of type Network

Modifier and Type	Method and Description
static boolean	NetworkTools.areEqual(Network a, Network b) 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.
static void	NetworkTools.dumpNetwork(Network net) Dumps the network to stdout.
static void	NetworkTools.dumpNetwork(Network net, Writer writer) Dumps the network to the given Writer.
static double	NetworkTools.getConstantBySettingReactantsToStoich(Network net, int r) Gets the reaction rate constant by setting the reactant amounts to the stoichiometric coefficient.
static String[]	NetworkTools.getReactionNames(Network net, int[] reaction) Transforms the reaction indices in the given array to the corresponding names.
static String	NetworkTools.getReactionNameWithAmounts(Network net, int... reactions) Gets a string representation of the given reactions and the amounts of each participating species in parentheses.
static int[]	NetworkTools.getReactionsOf(Network net, String[] speciesName) Gets the reaction whose products / reactants are in speciesName
static int[]	NetworkTools.getSpeciesIndices(Network net, String[] speciesName) Transforms the species names in the given array to the corresponding indices.
static String[]	NetworkTools.getSpeciesNames(Network net, int[] species) Transforms the species indices in the given array to the corresponding names.
static String	NetworkTools.getSpeciesNameWithAmount(Network net, int... species) Gets the species names together with its actual amount in parentheses
static void	NetworkTools.useActualAmountAsInitialAmount(Network net) Copies the actual amount of the species in the network to its initial amount.