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Packages that use CatalyzedFluxome | |
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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.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 |
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Subinterfaces of CatalyzedFluxome in sbrt.kernel.fba | |
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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 | |
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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 | |
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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 |
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Classes in sbrt.kernel.fba.proc with type parameters of type CatalyzedFluxome | |
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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 | |
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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 |
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Methods in sbrt.shell.mng.fba with parameters of type CatalyzedFluxome | |
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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 |
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Methods in sbrt.shell.text.fba that return CatalyzedFluxome | |
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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 | |
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CatalystListFormatV1(CatalyzedFluxome fluxome)
Constructs a new catalyst name collection format using the provided fluxome. |
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CatalystSetFormatV1(CatalyzedFluxome fluxome)
Constructs a new catalyst name collection format using the provided fluxome. |
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CatalystVerifier(CatalyzedFluxome fluxome)
Constructs a new catalyst name verifier for the provided fluxome. |
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