Uses of Package
fern.network

Packages that use fern.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.example Contains examples and demonstrations of the framework. 
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. 
 

Classes in fern.network used by fern.analysis
Network
          The central interface of the whole framework.
 

Classes in fern.network used by fern.benchmark
Network
          The central interface of the whole framework.
 

Classes in fern.network used by fern.cellDesigner
AbstractNetworkImpl
          Base implementation for the Network interface.
AmountManager
          The AmountManager is one of the most important connections between a Network and a Simulator.
ComplexDependenciesPropensityCalculator
          In a SBML network, the propensities of reaction are calculated by using the kineticLaw tag, which contains a MathML expression.
Network
          The central interface of the whole framework.
PropensityCalculator
          A PropensityCalculator is the way, a Network tells a Simulator how to calculate propensities for the reactions.
 

Classes in fern.network used by fern.cellDesigner.ui
Network
          The central interface of the whole framework.
 

Classes in fern.network used by fern.cytoscape
AbstractNetworkImpl
          Base implementation for the Network interface.
AnnotationManager
          AnnotationManager objects are the places, where static (or quasi-static) properties of a network are stored.
Network
          The central interface of the whole framework.
 

Classes in fern.network used by fern.example
FeatureNotSupportedException
           
 

Classes in fern.network used by fern.network
AbstractKineticConstantPropensityCalculator
          Base implementation of a PropensityCalculator.
AmountManager
          The AmountManager is one of the most important connections between a Network and a Simulator.
AnnotationManager
          AnnotationManager objects are the places, where static (or quasi-static) properties of a network are stored.
FeatureNotSupportedException
           
KineticConstantPropensityCalculator
           
Network
          The central interface of the whole framework.
PartialDerivativePropensityCalculator
           
PropensityCalculator
          A PropensityCalculator is the way, a Network tells a Simulator how to calculate propensities for the reactions.
 

Classes in fern.network used by fern.network.creation
AbstractNetworkImpl
          Base implementation for the Network interface.
Network
          The central interface of the whole framework.
PropensityCalculator
          A PropensityCalculator is the way, a Network tells a Simulator how to calculate propensities for the reactions.
 

Classes in fern.network used by fern.network.fernml
AbstractNetworkImpl
          Base implementation for the Network interface.
AnnotationManager
          AnnotationManager objects are the places, where static (or quasi-static) properties of a network are stored.
ArrayKineticConstantPropensityCalculator
          Implementation of an AbstractKineticConstantPropensityCalculator which uses an array to store the constants for each reaction.
Network
          The central interface of the whole framework.
 

Classes in fern.network used by fern.network.modification
AmountManager
          The AmountManager is one of the most important connections between a Network and a Simulator.
AnnotationManager
          AnnotationManager objects are the places, where static (or quasi-static) properties of a network are stored.
Network
          The central interface of the whole framework.
PropensityCalculator
          A PropensityCalculator is the way, a Network tells a Simulator how to calculate propensities for the reactions.
 

Classes in fern.network used by fern.network.sbml
AbstractNetworkImpl
          Base implementation for the Network interface.
AmountManager
          The AmountManager is one of the most important connections between a Network and a Simulator.
ComplexDependenciesPropensityCalculator
          In a SBML network, the propensities of reaction are calculated by using the kineticLaw tag, which contains a MathML expression.
FeatureNotSupportedException
           
Network
          The central interface of the whole framework.
PropensityCalculator
          A PropensityCalculator is the way, a Network tells a Simulator how to calculate propensities for the reactions.
 

Classes in fern.network used by fern.simulation
Network
          The central interface of the whole framework.
PropensityCalculator
          A PropensityCalculator is the way, a Network tells a Simulator how to calculate propensities for the reactions.
 

Classes in fern.network used by fern.simulation.algorithm
Network
          The central interface of the whole framework.
 

Classes in fern.network used by fern.tools
FeatureNotSupportedException
           
Network
          The central interface of the whole framework.