Uses of Interface
fern.network.Network

Packages that use Network
fern.analysis Provides classes and algorithms for analysing networks like ShortestPath, AutocatalyticDetection. 
fern.benchmark Provides classes for benchmarking simulations (time benchmarks, histogram distance calculation). 
fern.cellDesigner   
fern.cellDesigner.ui   
fern.cytoscape Provides the classes for the cytoscape plugin. 
fern.cytoscape.ui   
fern.network Provides general classes and interfaces for storing network data. 
fern.network.creation Provides classes for the evolution of networks. 
fern.network.fernml Provides the classes for parsing and using FernML based networks. 
fern.network.modification Provides classes for modifications of networks. 
fern.network.sbml Provides the classes for parsing and using sbml based networks. 
fern.simulation Provides algorithms for simulating reaction network as well as methods for observer certain aspects of a simulation. 
fern.simulation.algorithm Provides algorithms for stochastic simultion of reaction networks. 
fern.tools Provides common used tools. 
 

Uses of Network in fern.analysis
 

Methods in fern.analysis with parameters of type Network
 boolean NodeChecker.checkReactionNode(Network network, int reaction)
           
 boolean NodeCheckerByAnnotation.checkReactionNode(Network network, int reaction)
           
 boolean NodeChecker.checkSpeciesNode(Network network, int species)
           
 boolean NodeCheckerByAnnotation.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
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
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.cellDesigner
 

Classes in fern.cellDesigner that implement Network
 class CellDesignerNetworkWrapper
           
 

Uses of Network in fern.cellDesigner.ui
 

Methods in fern.cellDesigner.ui with parameters of type Network
 void MainFrame.loadNetwork(Network net)
           
 void OverviewPane.setErrorMessage(Network net, String message)
           
 void ExtendedPane.setSpecies(Network net)
           
 

Uses of Network in fern.cytoscape
 

Classes in fern.cytoscape that implement Network
 class CytoscapeNetworkWrapper
           
 

Uses of Network in fern.cytoscape.ui
 

Methods in fern.cytoscape.ui with parameters of type Network
 void MainFrame.loadNetwork(Network net)
           
 void OverviewPane.setErrorMessage(Network net, String message)
           
 void ExtendedPane.setSpecies(Network net)
           
 

Uses of Network in fern.network
 

Classes in fern.network that implement Network
 class AbstractNetworkImpl
          Base implementation for the Network interface.
 

Methods in fern.network that return Network
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
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
 class AutocatalyticNetwork
          Evolve an autocatalytic network.
 

Uses of Network in fern.network.fernml
 

Classes in fern.network.fernml that implement Network
 class FernMLNetwork
          A FernMLNetwork is usually loaded from a file.
 

Constructors in fern.network.fernml with parameters of type Network
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
 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 MultiplierNetwork
          Multiplies the whole network by a factor.
 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
 Network ModifierNetwork.getOriginalNetwork()
          Gets the original network.
 Network ModifierNetwork.getParentNetwork()
          Gets the parent network.
 

Constructors in fern.network.modification with parameters of type Network
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.
MultiplierNetwork(Network originalNet, int factor)
          Creates a new network from an original network and virtually multiplies each reaction and species factor times.
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
 class SBMLNetwork
          For specifications of the sbml format refer to http:\\www.sbml.org.
 

Constructors in fern.network.sbml with parameters of type Network
MathTree(Network net, org.sbml.libsbml.ASTNode ast, Map<String,Double> globals, Map<String,Double> locals, Map<String,Integer> bindings)
          Creates a MathTree from an libsbml ASTNode.
SBMLNetwork(Network net)
          Create a SBMLNetwork from an existing Network.
 

Uses of Network in fern.simulation
 

Methods in fern.simulation that return Network
 Network Simulator.getNet()
          Gets the simulation network.
 

Constructors in fern.simulation with parameters of type Network
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
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
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
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.