Uses of Interface
sbrt.kernel.fba.CatalyzedFluxome

Packages that use CatalyzedFluxome
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.mng.fba Provides classes and interfaces for creating Flux Balance Analysis process managers. 
sbrt.shell.text.fba Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis. 
 

Uses of CatalyzedFluxome in sbrt.kernel.fba
 

Subinterfaces of CatalyzedFluxome in sbrt.kernel.fba
 interface IrrevRxnFluxome
          This interface is used to represent fluxomes that contain only irreversible reactions.
 interface MixedFluxome
          This interface is used to represent fluxomes that contain multiple types of chemical reactions.
 

Classes in sbrt.kernel.fba that implement CatalyzedFluxome
 class IrrevRxnFluxomeV1
          This class is a concrete implementation of IrrevRxnFluxome.
 class MixedFluxomeV1
          This class is a concrete implementation of MixedFluxome.
 

Methods in sbrt.kernel.fba that return CatalyzedFluxome
 CatalyzedFluxome CatalyzedFluxome.replaceConstraints(FluxConstraints constraints, double constraintTolerance)
          Returns a copy of this fluxome, but with all constraints replaced by those provided.
 

Uses of CatalyzedFluxome in sbrt.kernel.fba.proc
 

Classes in sbrt.kernel.fba.proc with type parameters of type CatalyzedFluxome
 class CatalystDeletionProcess<F extends CatalyzedFluxome>
          This class is used to perform catalyst deletion processes.
 class CvCatalystDeletionProcess<F extends CatalyzedFluxome>
          This class is used to perform constraint-variation catalyst deletion processes.
 class NetworkInfoProcess<F extends CatalyzedFluxome>
          This class is used to gather basic information about a fluxome.
static class NetworkInfoProcess.Results<F extends CatalyzedFluxome>
          This class is used to represent the information gathered about a fluxome.
 

Methods in sbrt.kernel.fba.proc with parameters of type CatalyzedFluxome
static java.util.Set<java.lang.String> CatalystDeletionProcess.getRxnNames(java.util.Set<java.lang.String> catalysts, CatalyzedFluxome fluxome)
          Returns the set of names of reactions whose activity depends on the provided set of catalysts.
 

Uses of CatalyzedFluxome in sbrt.shell.mng.fba
 

Methods in sbrt.shell.mng.fba with parameters of type CatalyzedFluxome
static InputFile<java.util.Set<java.lang.String>> CatalystDeletionManager.getDeletionFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, CatalyzedFluxome fluxome)
          Parses and returns the value for CatalystDeletionManager.CATALYST_DELETION_FILE in the provided manager input.
static InputFile<java.util.Set<java.lang.String>> CatalystDeletionManager.getDeletionFile(java.lang.String fileName, CatalyzedFluxome fluxome)
          Returns the catalyst input file with the provided name.
 

Uses of CatalyzedFluxome in sbrt.shell.text.fba
 

Methods in sbrt.shell.text.fba that return CatalyzedFluxome
 CatalyzedFluxome CatalystVerifier.getFluxome()
          Returns the fluxome used to create this catalyst name verifier.
 CatalyzedFluxome CatalystListFormatV1.getFluxome()
          Returns the fluxome used to verify catalyst names.
 CatalyzedFluxome CatalystSetFormatV1.getFluxome()
          Returns the fluxome used to verify catalyst names.
 CatalyzedFluxome CatalystListFormat.getFluxome()
          Returns the fluxome used to verify catalyst names.
 

Constructors in sbrt.shell.text.fba with parameters of type CatalyzedFluxome
CatalystListFormatV1(CatalyzedFluxome fluxome)
          Constructs a new catalyst name collection format using the provided fluxome.
CatalystSetFormatV1(CatalyzedFluxome fluxome)
          Constructs a new catalyst name collection format using the provided fluxome.
CatalystVerifier(CatalyzedFluxome fluxome)
          Constructs a new catalyst name verifier for the provided fluxome.