Uses of Interface
fern.network.AmountManager

Packages that use AmountManager
fern.cellDesigner   
fern.network Provides general classes and interfaces for storing network data. 
fern.network.modification Provides classes for modifications of networks. 
fern.network.sbml Provides the classes for parsing and using sbml based networks. 
 

Uses of AmountManager in fern.cellDesigner
 

Methods in fern.cellDesigner with parameters of type AmountManager
 double CellDesignerPropensityCalculator.calculatePropensity(int reaction, AmountManager amount, Simulator sim)
           
 

Uses of AmountManager in fern.network
 

Classes in fern.network that implement AmountManager
 class ConstantAmountManager
           
 class DefaultAmountManager
          Default implementation of an amount manager, that stores the amounts in arrays.
 

Methods in fern.network that return AmountManager
 AmountManager AbstractNetworkImpl.getAmountManager()
           
 AmountManager Network.getAmountManager()
          Gets the AmountManager for this network.
 

Methods in fern.network with parameters of type AmountManager
 double AbstractKineticConstantPropensityCalculator.calculatePartialDerivative(int reaction, AmountManager amount, int reactantIndex, double volume)
          Calculates partial differentials of the propensity functions for the tau leaping methods.
 double PartialDerivativePropensityCalculator.calculatePartialDerivative(int reaction, AmountManager amount, int reactantIndex, double volume)
          Calculates partial differentials of the propensity functions for the tau leaping methods.
 double AbstractKineticConstantPropensityCalculator.calculatePropensity(int reaction, AmountManager amount, Simulator sim)
          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.
 double PropensityCalculator.calculatePropensity(int reaction, AmountManager amount, Simulator sim)
          Calculates the propensity for a reaction given the amounts of the AmountManager.
 

Uses of AmountManager in fern.network.modification
 

Methods in fern.network.modification that return AmountManager
 AmountManager ExtractSubNetwork.getAmountManager()
          Gets the AmountManager for the extracted subnet.
 AmountManager ModifierNetwork.getAmountManager()
          Gets the AmountManager of the original network.
 AmountManager CatalysedNetwork.getAmountManager()
           
 AmountManager ReversibleNetwork.getAmountManager()
          Gets the AmountManager for the modified network.
 AmountManager MultiplierNetwork.getAmountManager()
          Gets the AmountManager for the modified network.
 

Uses of AmountManager in fern.network.sbml
 

Methods in fern.network.sbml with parameters of type AmountManager
 double MathTree.calculate(AmountManager amount, Simulator sim)
          Evaluate the MathTree.
 double SBMLPropensityCalculator.calculatePropensity(int reaction, AmountManager amount, Simulator sim)