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Packages that use IrrevRxnFluxome | |
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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 |
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Classes in sbrt.kernel.fba that implement IrrevRxnFluxome | |
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class |
IrrevRxnFluxomeV1
This class is a concrete implementation of IrrevRxnFluxome . |
Methods in sbrt.kernel.fba that return IrrevRxnFluxome | |
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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 | |
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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 |
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Classes in sbrt.kernel.fba.comp with type parameters of type IrrevRxnFluxome | |
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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 | |
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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 | |
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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 | |
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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. |
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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 |
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Classes in sbrt.kernel.fba.proc with type parameters of type IrrevRxnFluxome | |
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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 | |
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IrrevRxnFluxome |
FluxCapProcess.getFluxome()
Returns the fluxome for which flux caps are computed. |
Constructors in sbrt.kernel.fba.proc with parameters of type IrrevRxnFluxome | |
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RedundRxnRemoverProcess(IrrevRxnFluxome fluxome)
Constructs a new redundant reaction remover process. |
Uses of IrrevRxnFluxome in sbrt.shell.mng.fba |
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Methods in sbrt.shell.mng.fba that return IrrevRxnFluxome | |
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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 | |
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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 | |
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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 |
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Methods in sbrt.shell.proc.fba with parameters of type IrrevRxnFluxome | |
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void |
MetatoolInputWriter.writeFile(IrrevRxnFluxome fluxome,
OutputFile<java.lang.String> file)
Writes a metatool input file. |
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