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Packages that use MixedFluxome | |
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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 MixedFluxome in sbrt.kernel.fba |
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Classes in sbrt.kernel.fba that implement MixedFluxome | |
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class |
MixedFluxomeV1
This class is a concrete implementation of MixedFluxome . |
Methods in sbrt.kernel.fba that return MixedFluxome | |
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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 | |
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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 |
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Methods in sbrt.kernel.fba.comp that return MixedFluxome | |
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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 | |
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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 |
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Constructors in sbrt.kernel.fba.proc with parameters of type MixedFluxome | |
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RedundRxnRemoverProcess(MixedFluxome fluxome)
Constructs a new redundant reaction remover process. |
Uses of MixedFluxome in sbrt.shell.mng.fba |
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Methods in sbrt.shell.mng.fba that return MixedFluxome | |
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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 | |
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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 | |
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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 |
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Methods in sbrt.shell.proc.fba with parameters of type MixedFluxome | |
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void |
MetatoolInputWriter.writeFile(MixedFluxome fluxome,
OutputFile<java.lang.String> file)
Writes a metatool input file. |
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