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Packages that use AmountManager | |
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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 |
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Methods in fern.cellDesigner with parameters of type AmountManager | |
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double |
CellDesignerPropensityCalculator.calculatePropensity(int reaction,
AmountManager amount,
Simulator sim)
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Uses of AmountManager in fern.network |
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Classes in fern.network that implement AmountManager | |
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class |
ConstantAmountManager
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class |
DefaultAmountManager
Default implementation of an amount manager, that stores the amounts in arrays. |
Methods in fern.network that return AmountManager | |
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AmountManager |
AbstractNetworkImpl.getAmountManager()
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AmountManager |
Network.getAmountManager()
Gets the AmountManager for this network. |
Methods in fern.network with parameters of type AmountManager | |
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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 |
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Methods in fern.network.modification that return AmountManager | |
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AmountManager |
ExtractSubNetwork.getAmountManager()
Gets the AmountManager for the extracted subnet. |
AmountManager |
ModifierNetwork.getAmountManager()
Gets the AmountManager of the original network. |
AmountManager |
CatalysedNetwork.getAmountManager()
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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 |
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Methods in fern.network.sbml with parameters of type AmountManager | |
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double |
MathTree.calculate(AmountManager amount,
Simulator sim)
Evaluate the MathTree. |
double |
SBMLPropensityCalculator.calculatePropensity(int reaction,
AmountManager amount,
Simulator sim)
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