Uses of Class
sbrt.kernel.fba.FluxConstraints

Packages that use FluxConstraints
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
 

Methods in sbrt.kernel.fba that return FluxConstraints
 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
 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
 

Methods in sbrt.kernel.fba.proc with parameters of type FluxConstraints
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
 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
 

Methods in sbrt.shell.io.fba that return FluxConstraints
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
 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
 

Methods in sbrt.shell.mng.fba that return FluxConstraints
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.