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See:
Description
Interface Summary | |
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CycleComputer<F extends Fluxome> | This interface is used to represent algorithms for identifying steady state cycles in stoichiometric networks. |
ExtremeCurrentComputer | This interface is used to represent extreme current computers. |
FluxCvComputer<F extends Fluxome> | This interface is used to represent a flux constraint variation computer. |
FluxIntervalComputer<F extends Fluxome> | This interface is used to represent flux interval computers. |
FluxomeReducer<T extends Fluxome> | This interface is used to represent algorithms that reduce the size of fluxomes. |
Class Summary | |
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AbstractCvComputer<F extends Fluxome> | This abstract class is a skeleton implementation of FluxCvComputer. |
AbstractFluxIntervalComputer<F extends Fluxome> | This abstract class is a skeleton implemenation of FluxIntervalComputer. |
CdHarFluxComp<F extends Fluxome> | This class is used to compute randomly distributed vectors within flux space. |
FbaOptimizer<F extends Fluxome> | This class is the workhorse of all Flux Balance Analysis optimizations. |
FbaSolver | This class is used to solve the system of linear equations Sv = 0. |
FluxCapComputer | This class is used to compute flux caps for use in Mahadevan-Schilling flux interval computations. |
InitialPointComputer<F extends Fluxome> | This class is used to compute initial points for coordinate-direction hit-and-run random flux vector algorithms. |
MsFluxIntervalComputer<F extends IrrevRxnFluxome> | This class is used to compute Mahadevan-Schilling flux intervals. |
MsFluxomeReducer | This class is used to reduce the size of fluxomes for the purpose of identifying the steady state cycles they contain. |
RedundRxnRemover | This class is used to remove "redundant" reactions from fluxomes. |
ReverseRxnIntervalComp<F extends IrrevRxnFluxome> | This class is used to compute flux intervals while constraining the fluxes of reverse reactions to their minimum. |
RxnDeletionComputer<F extends Fluxome> | This class is used to compute the effect of deleting reactions in a fluxome. |
SimpleFluxIntervalComputer<F extends Fluxome> | This class is used to compute flux intervals in the simplest possible way. |
SlpCycleComputer | This class is used to identify the steady state cycles in stoichiometric networks. |
SlpExCurrComputerV2 | This class is an implementation of an algorithm for identifying extreme currents in stoichiometric networks. |
WwFluxomeReducer | This class is used to reduce the size of fluxomes for the purpose of identifying the steady state cycles they contain. |
Exception Summary | |
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FbaOptException | This class is used to indicate that an optimal solution could not be found or does not exist. |
FluxCapException | This class is used to indicate that a flux cap is invalid. |
FluxRangeException | This class is used to indicate that the range of a flux interval has exceeded a defined cutoff value. |
InvalidFluxVectorException | This class is used to indicate that a flux vector is invalid. |
Provides classes and interfaces for performing Flux Balance Analysis computations.
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