Package sbrt.kernel.fba.comp

Provides classes and interfaces for performing Flux Balance Analysis computations.

See:
          Description

Interface Summary
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
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
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.
 

Package sbrt.kernel.fba.comp Description

Provides classes and interfaces for performing Flux Balance Analysis computations.