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Packages that use FluxConstraints | |
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sbrt.kernel.fba | Provides classes and interfaces for creating objects relevant to Flux Balance Analysis. |
sbrt.kernel.fba.proc | Provides classes and interfaces for executing Flux Balance Analysis processes. |
sbrt.shell.io.fba | Provides classes and interfaces for reading and writing files relevant to Flux Balance Analysis. |
sbrt.shell.mng.fba | Provides classes and interfaces for creating Flux Balance Analysis process managers. |
Uses of FluxConstraints in sbrt.kernel.fba |
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Methods in sbrt.kernel.fba that return FluxConstraints | |
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FluxConstraints |
MixedFluxomeV1.getConstraints()
Returns all constraints in this fluxome. |
FluxConstraints |
Fluxome.getConstraints()
Returns the set of all constraints for fluxes and mathematical expressions of fluxes in this fluxome. |
FluxConstraints |
IrrevRxnFluxomeV1.getConstraints()
Returns all constraints in this fluxome. |
Methods in sbrt.kernel.fba with parameters of type FluxConstraints | |
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MixedFluxomeV1 |
MixedFluxomeV1.replaceConstraints(FluxConstraints fluxConstraints,
double constraintTolerance)
Returns a copy of this fluxome, but with all constraints replaced by those provided. |
IrrevRxnFluxome |
IrrevRxnFluxome.replaceConstraints(FluxConstraints constraints,
double constraintTolerance)
Returns a copy of this fluxome, but with all constraints replaced by those provided. |
Fluxome |
Fluxome.replaceConstraints(FluxConstraints constraints,
double constraintTolerance)
Returns a copy of this fluxome, but with all constraints replaced by those provided. |
IrrevRxnFluxomeV1 |
IrrevRxnFluxomeV1.replaceConstraints(FluxConstraints fluxConstraints,
double constraintTolerance)
Returns a copy of this fluxome, but with all constraints replaced by those provided. |
MixedFluxome |
MixedFluxome.replaceConstraints(FluxConstraints constraints,
double constraintTolerance)
Returns a copy of this fluxome, but with all constraints replaced by those provided. |
CatalyzedFluxome |
CatalyzedFluxome.replaceConstraints(FluxConstraints constraints,
double constraintTolerance)
Returns a copy of this fluxome, but with all constraints replaced by those provided. |
Uses of FluxConstraints in sbrt.kernel.fba.proc |
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Methods in sbrt.kernel.fba.proc with parameters of type FluxConstraints | |
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static void |
CvRxnDeletionProcess.checkForConflict(FluxConstraints fc,
java.util.Set<java.lang.String> deletionNames)
Ensures that the provided flux constraints and set of reaction names do not conflict. |
static void |
AbstractCvFbaOptProcess.restoreConstraints(FluxConstraints constraints,
FluxCvComputer<?> computer)
Restores the provided constraints in the provided constraint-variation computer. |
static void |
AbstractCvFbaOptProcess.setConstraints(FluxConstraints constraints,
FluxCvComputer<?> computer)
Sets the provided constraints in the provided constraint-variation computer. |
Method parameters in sbrt.kernel.fba.proc with type arguments of type FluxConstraints | |
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void |
CvFbaOptProcess.setConstraintSource(java.lang.Iterable<FluxConstraints> constraintSource)
Sets the constraint variation input source. |
void |
CvRxnDeletionProcess.setConstraintSource(java.lang.Iterable<FluxConstraints> constraintSource)
Sets the constraint variation input source. |
void |
CvObjectiveFunctionProcess.setConstraintSource(java.lang.Iterable<FluxConstraints> constraintSource)
Sets the constraint variation input source. |
void |
CvFluxIntervalProcess.setConstraintSource(java.lang.Iterable<FluxConstraints> constraintSource)
Sets the constraint variation input source. |
void |
CvCatalystDeletionProcess.setConstraintSource(java.lang.Iterable<FluxConstraints> constraintSource)
Sets the constraint variation input source. |
void |
SvInitialPointProcess.setIntervalSource(java.lang.Iterable<FluxConstraints> intervalSource)
Sets the flux interval input source. |
void |
SvCdHarFluxVectorProcess.setIntervalSource(java.lang.Iterable<FluxConstraints> intervalSource)
Sets the flux interval input source. |
Uses of FluxConstraints in sbrt.shell.io.fba |
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Methods in sbrt.shell.io.fba that return FluxConstraints | |
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static FluxConstraints |
FluxIntervalInputFile.convertConstraints(java.util.Map<LinearComb<java.lang.String>,Interval> intervals,
Fluxome fluxome,
double tolerance)
Converts the provided intervals into a FluxConstraints object. |
Methods in sbrt.shell.io.fba that return types with arguments of type FluxConstraints | |
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java.util.Iterator<FluxConstraints> |
FluxIntervalInputFile.iterator()
Returns an iterator over the flux intervals contained in this file. |
Uses of FluxConstraints in sbrt.shell.mng.fba |
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Methods in sbrt.shell.mng.fba that return FluxConstraints | |
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static FluxConstraints |
FbaOptManager.getConstraints(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Opens the file denoted by FbaOptManager.CONSTRAINTS_FILE in the provided manager input and returns the set of flux constraints it contains. |
static FluxConstraints |
RandomFluxVectorManager.getConstraints(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Opens the file denoted by FbaOptManager.CONSTRAINTS_FILE in the provided manager input and returns the set of flux constraints it contains. |
static FluxConstraints |
FbaOptManager.getConstraints(java.lang.String fileName,
Fluxome fluxome,
double tolerance)
Returns the set of constraints contained in the file with the provided name. |
static FluxConstraints |
RandomFluxVectorManager.getConstraints(java.lang.String fileName,
Fluxome fluxome,
double tolerance)
Returns the set of constraints contained in the file with the provided name. |
static FluxConstraints |
InitialPointManager.getIntervals(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Opens the file denoted by InitialPointManager.FLUX_INTERVAL_FILE in the provided manager input and returns the set of flux intervals it contains. |
static FluxConstraints |
InitialPointManager.getIntervals(java.lang.String fileName,
Fluxome fluxome,
double tolerance)
Returns the set of flux intervals contained in the file with the provided name. |
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