Uses of Interface
sbrt.kernel.fba.IrrevRxnFluxome

Packages that use IrrevRxnFluxome
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 IrrevRxnFluxome in sbrt.kernel.fba
 

Classes in sbrt.kernel.fba that implement IrrevRxnFluxome
 class IrrevRxnFluxomeV1
          This class is a concrete implementation of IrrevRxnFluxome.
 

Methods in sbrt.kernel.fba that return IrrevRxnFluxome
 IrrevRxnFluxome IrrevRxnFluxome.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 IrrevRxnFluxome
static IrrevRxnFluxomeV1 IrrevRxnFluxomeV1.make(java.util.Collection<java.lang.String> reactionNames, IrrevRxnFluxome fluxome)
          Returns an irreversible reaction fluxome composed of the reactions in the provided fluxome with the names in the provided collection.
 

Uses of IrrevRxnFluxome in sbrt.kernel.fba.comp
 

Classes in sbrt.kernel.fba.comp with type parameters of type IrrevRxnFluxome
 class MsFluxIntervalComputer<F extends IrrevRxnFluxome>
          This class is used to compute Mahadevan-Schilling flux intervals.
 class ReverseRxnIntervalComp<F extends IrrevRxnFluxome>
          This class is used to compute flux intervals while constraining the fluxes of reverse reactions to their minimum.
 

Methods in sbrt.kernel.fba.comp that return IrrevRxnFluxome
 IrrevRxnFluxome FluxCapComputer.getFluxome()
          Returns the fluxome for which flux caps are computed.
 IrrevRxnFluxome MsFluxomeReducer.makeFluxome(IrrevRxnFluxome fluxome)
          Returns the sub-fluxome resulting from network reduction.
 IrrevRxnFluxome WwFluxomeReducer.makeFluxome(IrrevRxnFluxome fluxome)
          Returns the sub-fluxome resulting from network reduction.
static IrrevRxnFluxome RedundRxnRemover.remove(IrrevRxnFluxome fluxome)
          Returns a fluxome for which all "redundant" reactions have been eliminated.
 

Methods in sbrt.kernel.fba.comp with parameters of type IrrevRxnFluxome
 SparseDoubleMatrix<?,java.lang.String> SlpCycleComputer.getCycles(IrrevRxnFluxome fluxome)
          Returns the set of all steady state cycles contained in the provided fluxome.
 SparseDoubleMatrix<?,java.lang.String> SlpExCurrComputerV2.getMatrix(IrrevRxnFluxome fluxome)
          Returns the extreme current matrix for the provided fluxome.
 SparseDoubleMatrix<?,java.lang.String> ExtremeCurrentComputer.getMatrix(IrrevRxnFluxome fluxome)
          Returns the extreme current matrix for the provided fluxome.
 SparseDoubleMatrix<?,java.lang.String> SlpExCurrComputerV2.getMatrix(IrrevRxnFluxome fluxome, MutableProgressMonitor pm)
          Returns the extreme current matrix for the provided fluxome.
 SparseDoubleMatrix<?,java.lang.String> ExtremeCurrentComputer.getMatrix(IrrevRxnFluxome fluxome, MutableProgressMonitor pm)
          Returns the extreme current matrix for the provided fluxome.
 int SlpExCurrComputerV2.getTotalOps(IrrevRxnFluxome fluxome)
          Returns the total number of "operations" required to compute the extreme currents of the provided fluxome.
 int ExtremeCurrentComputer.getTotalOps(IrrevRxnFluxome fluxome)
          Returns the total number of "operations" required to compute the extreme currents of the provided fluxome.
 IrrevRxnFluxome MsFluxomeReducer.makeFluxome(IrrevRxnFluxome fluxome)
          Returns the sub-fluxome resulting from network reduction.
 IrrevRxnFluxome WwFluxomeReducer.makeFluxome(IrrevRxnFluxome fluxome)
          Returns the sub-fluxome resulting from network reduction.
static IrrevRxnFluxome RedundRxnRemover.remove(IrrevRxnFluxome fluxome)
          Returns a fluxome for which all "redundant" reactions have been eliminated.
 

Constructors in sbrt.kernel.fba.comp with parameters of type IrrevRxnFluxome
FluxCapComputer(IrrevRxnFluxome fluxome, java.util.Collection<LinearComb<java.lang.String>> allCycles)
          Constructs a new flux cap computer from the cycles contained in the provided fluxome.
FluxCapComputer(IrrevRxnFluxome fluxome, DoubleMatrix<?,java.lang.String> cycleMatrix)
          Constructs a new flux cap computer from the cycles contained in the provided fluxome.
 

Uses of IrrevRxnFluxome in sbrt.kernel.fba.proc
 

Classes in sbrt.kernel.fba.proc with type parameters of type IrrevRxnFluxome
 class ExtremeCurrentProcess<F extends IrrevRxnFluxome>
          This class is used to identify the extreme currents in stoichiometric networks.
 

Methods in sbrt.kernel.fba.proc that return IrrevRxnFluxome
 IrrevRxnFluxome FluxCapProcess.getFluxome()
          Returns the fluxome for which flux caps are computed.
 

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

Uses of IrrevRxnFluxome in sbrt.shell.mng.fba
 

Methods in sbrt.shell.mng.fba that return IrrevRxnFluxome
static IrrevRxnFluxome FbaOptManager.getIrrevRxnFluxome(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Creates and returns a fluxome based on the provided input.
static IrrevRxnFluxome FbaManager.getIrrevRxnFluxome(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 IrrevRxnFluxome RandomFluxVectorManager.getIrrevRxnFluxome(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Creates and returns a fluxome based on the provided input.
static IrrevRxnFluxome FbaOptManager.getIrrevRxnFluxome(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 IrrevRxnFluxome FbaManager.getIrrevRxnFluxome(java.lang.String fileName)
          Returns the fluxome contained in the file with the provided name.
static IrrevRxnFluxome FbaManager.getIrrevRxnFluxome(java.lang.String fileName, java.io.PrintWriter out)
          Returns the fluxome contained in the file with the provided name.
static IrrevRxnFluxome FbaManager.getIrrevRxnFluxome(java.lang.String rxnFileName, java.lang.String catalystFileName)
          Returns the fluxome contained in the files with the provided names.
static IrrevRxnFluxome FbaManager.getIrrevRxnFluxome(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 IrrevRxnFluxome
static ReverseRxnIntervalComp<IrrevRxnFluxome> ReverseRxnFluxIntervalManager.getComputer(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Returns the flux interval computer specified by the provided input.
static MsFluxIntervalComputer<IrrevRxnFluxome> MsFluxIntervalManager.getIrrevComp(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Returns the flux interval computer specified by the provided input.
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.
 FluxomeReducerProcess<IrrevRxnFluxome> WwFluxomeReducerManager.getProcess()
          Returns the process this process manager controls.
 ExtremeCurrentProcess<IrrevRxnFluxome> ExtremeCurrentManager.getProcess()
          Returns the process this process manager controls.
 FluxIntervalProcess<IrrevRxnFluxome> ReverseRxnFluxIntervalManager.getProcess()
          Returns the process this process manager controls.
 CycleIdProcess<IrrevRxnFluxome> SlpCycleIdManager.getProcess()
          Returns the process this process manager controls.
 FluxomeReducerProcess<IrrevRxnFluxome> MsFluxomeReducerManager.getProcess()
          Returns the process this process manager controls.
 CvFluxIntervalProcess<IrrevRxnFluxome> CvRevRxnFluxIntervalManager.getProcess()
          Returns the process this process manager controls.
 FluxIntervalProcess<IrrevRxnFluxome> MsFluxIntervalManager.getProcess()
          Returns the process this process manager controls.
 CvFluxIntervalProcess<IrrevRxnFluxome> CvMsFluxIntervalManager.getProcess()
          Returns the process this process manager controls.
 

Methods in sbrt.shell.mng.fba with parameters of type IrrevRxnFluxome
static MapTextOutputFile<java.lang.String,Interval> RandomConstraintsManager.getOutputFile(java.lang.String fileName, java.util.Set<java.lang.String> headers, IrrevRxnFluxome fluxome)
          Returns an empty output file that is suitable for storing multiple sets of flux constraints.
static void FbaManager.writeFluxome(IrrevRxnFluxome fluxome, java.lang.String fileName)
          Writes the provided fluxome to a file with the provided name.
static void FbaManager.writeFluxome(IrrevRxnFluxome fluxome, java.lang.String fileName, java.io.PrintWriter out)
          Writes the provided fluxome to a file with the provided name.
 

Uses of IrrevRxnFluxome in sbrt.shell.proc.fba
 

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