Uses of Class
sbrt.kernel.fba.comp.FbaOptimizer

Packages that use FbaOptimizer
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
 

Constructors in sbrt.kernel.fba.comp with parameters of type FbaOptimizer
AbstractFluxIntervalComputer(FbaOptimizer<F> computer)
          Constructs a new flux interval computer with the default zero cutoff.
AbstractFluxIntervalComputer(FbaOptimizer<F> computer, double zeroCutoff)
          Constructs a new flux interval computer with the provided zero cutoff.
InitialPointComputer(FbaOptimizer<F> computer)
          Constructs a new initial point, or flux vector, computer.
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.
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.
ReverseRxnIntervalComp(FbaOptimizer<F> computer, double zeroCutoff)
          Constructs a new flux interval computer.
RxnDeletionComputer(FbaOptimizer<F> computer)
          Constructs a new reaction deletion computer.
SimpleFluxIntervalComputer(FbaOptimizer<F> computer, double zeroCutoff)
          Constructs a new flux interval computer.
 

Uses of FbaOptimizer in sbrt.kernel.fba.proc
 

Constructors in sbrt.kernel.fba.proc with parameters of type FbaOptimizer
CvFbaOptProcess(FbaOptimizer<F> computer)
          Constructs a new constraint-variation FBA optimization process.
CvObjectiveFunctionProcess(FbaOptimizer<F> computer)
          Constructs a new constraint-variation objective function process.
FbaOptProcess(FbaOptimizer<F> computer)
          Constructs a new FBA optimization process.
ObjFunAnalysis(FbaOptimizer<F> computer)
          Constructs a new objective function process.
 

Uses of FbaOptimizer in sbrt.shell.mng.fba
 

Methods in sbrt.shell.mng.fba that return FbaOptimizer
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.