Uses of Interface
sbrt.kernel.fba.MixedFluxome

Packages that use MixedFluxome
sbrt.kernel.fba Provides classes and interfaces for creating objects relevant to Flux Balance Analysis. 
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. 
sbrt.shell.proc.fba Provides classes for converting FBA-related files of different formats. 
 

Uses of MixedFluxome in sbrt.kernel.fba
 

Classes in sbrt.kernel.fba that implement MixedFluxome
 class MixedFluxomeV1
          This class is a concrete implementation of MixedFluxome.
 

Methods in sbrt.kernel.fba that return MixedFluxome
 MixedFluxome MixedFluxome.replaceConstraints(FluxConstraints constraints, double constraintTolerance)
          Returns a copy of this fluxome, but with all constraints replaced by those provided.
 

Methods in sbrt.kernel.fba with parameters of type MixedFluxome
static MixedFluxomeV1 MixedFluxomeV1.make(java.util.Collection<java.lang.String> reactionNames, MixedFluxome fluxome)
          Returns a mixed fluxome composed of the reactions in the provided fluxome with the names in the provided collection.
 

Uses of MixedFluxome in sbrt.kernel.fba.comp
 

Methods in sbrt.kernel.fba.comp that return MixedFluxome
static MixedFluxome RedundRxnRemover.remove(MixedFluxome fluxome)
          Returns a fluxome for which all "redundant" reactions have been eliminated.
 

Methods in sbrt.kernel.fba.comp with parameters of type MixedFluxome
static MixedFluxome RedundRxnRemover.remove(MixedFluxome fluxome)
          Returns a fluxome for which all "redundant" reactions have been eliminated.
 

Uses of MixedFluxome in sbrt.kernel.fba.proc
 

Constructors in sbrt.kernel.fba.proc with parameters of type MixedFluxome
RedundRxnRemoverProcess(MixedFluxome fluxome)
          Constructs a new redundant reaction remover process.
 

Uses of MixedFluxome in sbrt.shell.mng.fba
 

Methods in sbrt.shell.mng.fba that return MixedFluxome
static MixedFluxome FbaOptManager.getMixedFluxome(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Creates and returns a fluxome based on the provided input.
static MixedFluxome FbaManager.getMixedFluxome(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Opens the file denoted by FbaManager.RXN_FILE in the provided manager input and returns the fluxome it contains.
static MixedFluxome FbaOptManager.getMixedFluxome(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, double tolerance)
          Creates and returns a fluxome based on the provided input.
static MixedFluxome InitialPointManager.getMixedFluxome(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, double tolerance)
          Creates and returns a fluxome based on the provided input.
static MixedFluxome FbaManager.getMixedFluxome(java.lang.String fileName)
          Returns the fluxome contained in the file with the provided name.
static MixedFluxome FbaManager.getMixedFluxome(java.lang.String fileName, java.io.PrintWriter out)
          Returns the fluxome contained in the file with the provided name.
static MixedFluxome FbaManager.getMixedFluxome(java.lang.String rxnFileName, java.lang.String catalystFileName)
          Returns the fluxome contained in the files with the provided names.
static MixedFluxome FbaManager.getMixedFluxome(java.lang.String rxnFileName, java.lang.String catalystFileName, java.io.PrintWriter out)
          Returns the fluxome contained in the files with the provided names.
 

Methods in sbrt.shell.mng.fba that return types with arguments of type MixedFluxome
static CdHarFluxComp<MixedFluxome> CdHarFluxVectorManager.getMixedComp(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Creates and returns a coordinate-direction hit-and-run flux vector computer using the provided input.
static SimpleFluxIntervalComputer<MixedFluxome> SimpleFluxIntervalManager.getMixedComp(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Returns the flux interval computer specified by 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.
static CdHarFluxComp<MixedFluxome> CdHarFluxVectorManager.getMixedComp(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, MixedFluxome fluxome, double tolerance)
          Creates and returns a coordinate-direction hit-and-run flux vector computer using the provided input.
static RxnDeletionComputer<MixedFluxome> RxnDeletionManager.getMixedDelComp(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Returns a reaction deletion computer created from the provided input.
 RandConstGeneratorV1<MixedFluxome> RandomConstraintsManager.getProcess()
          Returns the process this process manager controls.
 CdHarFluxVectorProcess<MixedFluxome> CdHarFluxVectorManager.getProcess()
          Returns the process this process manager controls.
 CvFbaOptProcess<MixedFluxome> CvFbaOptManager.getProcess()
          Returns the process this process manager controls.
 NetworkInfoProcess<MixedFluxome> NetworkInfoManager.getProcess()
          Returns the process this process manager controls.
 FluxIntervalProcess<MixedFluxome> SimpleFluxIntervalManager.getProcess()
          Returns the process this process manager controls.
 FbaOptProcess<MixedFluxome> FbaOptManager.getProcess()
          Returns the process this process manager controls.
 RxnDeletionProcess<MixedFluxome> RxnDeletionManager.getProcess()
          Returns the process this process manager controls.
 CvRxnDeletionProcess<MixedFluxome> CvRxnDeletionManager.getProcess()
          Returns the process this process manager controls.
 ObjFunAnalysis<MixedFluxome> ObjectiveFunctionManager.getProcess()
          Returns the process this process manager controls.
 CvCatalystDeletionProcess<MixedFluxome> CvCatalystDeletionManager.getProcess()
          Returns the process this process manager controls.
 FbaSolverProcess<MixedFluxome> FbaSolverManager.getProcess()
          Returns the process this process manager controls.
 FluxPlasticityProcess<MixedFluxome> FluxPlasticityManager.getProcess()
          Returns the process this process manager controls.
 RandomObjectiveGenerator<MixedFluxome> RandomObjectiveManager.getProcess()
          Returns the process this process manager controls.
 CvFluxIntervalProcess<MixedFluxome> CvSimpleFluxIntervalManager.getProcess()
          Returns the process this process manager controls.
 CatalystDeletionProcess<MixedFluxome> CatalystDeletionManager.getProcess()
          Returns the process this process manager controls.
 InitialPointGenerator<MixedFluxome> InitialPointManager.getProcess()
          Returns the process this process manager controls.
 CvObjectiveFunctionProcess<MixedFluxome> CvObjectiveFunctionManager.getProcess()
          Returns the process this process manager controls.
 FluxActivityProcess<MixedFluxome> FluxActivityManager.getProcess()
          Returns the process this process manager controls.
 

Methods in sbrt.shell.mng.fba with parameters of type MixedFluxome
static CdHarFluxComp<MixedFluxome> CdHarFluxVectorManager.getMixedComp(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, MixedFluxome fluxome, double tolerance)
          Creates and returns a coordinate-direction hit-and-run flux vector computer using the provided input.
static void NetworkInfoManager.printBasicInfo(MixedFluxome fluxome, java.io.PrintWriter out)
          Prints basic information about the provided fluxome.
static void FbaManager.writeFluxome(MixedFluxome fluxome, java.lang.String fileName)
          Writes the provided fluxome to a file with the provided name.
static void FbaManager.writeFluxome(MixedFluxome fluxome, java.lang.String fileName, java.io.PrintWriter out)
          Writes the provided fluxome to a file with the provided name.
 

Uses of MixedFluxome in sbrt.shell.proc.fba
 

Methods in sbrt.shell.proc.fba with parameters of type MixedFluxome
 void MetatoolInputWriter.writeFile(MixedFluxome fluxome, OutputFile<java.lang.String> file)
          Writes a metatool input file.