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Packages that use FbaOptimizer | |
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sbrt.kernel.fba.comp | Provides classes and interfaces for performing Flux Balance Analysis computations. |
sbrt.kernel.fba.proc | Provides classes and interfaces for executing Flux Balance Analysis processes. |
sbrt.shell.mng.fba | Provides classes and interfaces for creating Flux Balance Analysis process managers. |
Uses of FbaOptimizer in sbrt.kernel.fba.comp |
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Constructors in sbrt.kernel.fba.comp with parameters of type FbaOptimizer | |
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AbstractFluxIntervalComputer(FbaOptimizer<F> computer)
Constructs a new flux interval computer with the default zero cutoff. |
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AbstractFluxIntervalComputer(FbaOptimizer<F> computer,
double zeroCutoff)
Constructs a new flux interval computer with the provided zero cutoff. |
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InitialPointComputer(FbaOptimizer<F> computer)
Constructs a new initial point, or flux vector, computer. |
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MsFluxIntervalComputer(FbaOptimizer<F> computer,
java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> fluxCaps)
Constructs a new Mahadevan-Schilling flux interval computer. |
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MsFluxIntervalComputer(FbaOptimizer<F> computer,
java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> fluxCaps,
double zeroCutoff)
Constructs a new Mahadevan-Schilling flux interval computer. |
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ReverseRxnIntervalComp(FbaOptimizer<F> computer,
double zeroCutoff)
Constructs a new flux interval computer. |
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RxnDeletionComputer(FbaOptimizer<F> computer)
Constructs a new reaction deletion computer. |
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SimpleFluxIntervalComputer(FbaOptimizer<F> computer,
double zeroCutoff)
Constructs a new flux interval computer. |
Uses of FbaOptimizer in sbrt.kernel.fba.proc |
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Constructors in sbrt.kernel.fba.proc with parameters of type FbaOptimizer | |
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CvFbaOptProcess(FbaOptimizer<F> computer)
Constructs a new constraint-variation FBA optimization process. |
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CvObjectiveFunctionProcess(FbaOptimizer<F> computer)
Constructs a new constraint-variation objective function process. |
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FbaOptProcess(FbaOptimizer<F> computer)
Constructs a new FBA optimization process. |
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ObjFunAnalysis(FbaOptimizer<F> computer)
Constructs a new objective function process. |
Uses of FbaOptimizer in sbrt.shell.mng.fba |
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Methods in sbrt.shell.mng.fba that return FbaOptimizer | |
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static FbaOptimizer<IrrevRxnFluxome> |
FbaOptManager.getIrrevRxnComp(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Creates and returns an FBA optimization computer based on the provided input. |
static FbaOptimizer<MixedFluxome> |
FbaOptManager.getMixedComp(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Creates and returns an FBA optimization computer based on the provided input. |
static FbaOptimizer<MixedFluxome> |
InitialPointManager.getMixedComp(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Creates and returns an FBA optimization computer based on the provided input. |
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