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PREV NEXT | FRAMES NO FRAMES |
Packages that use ManagerInput | |
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plug_in_example.shell | |
sbrt | Provides the class used to run the Systems Biology Research Tool. |
sbrt.shell | Provides classes used by shell-level software. |
sbrt.shell.io | Provides classes and interfaces for reading and writing files. |
sbrt.shell.mng | Provides classes and interfaces for creating process managers. |
sbrt.shell.mng.algebra | Provides classes for creating algebra process managers. |
sbrt.shell.mng.comb | Provides classes for creating combinatorics process managers. |
sbrt.shell.mng.fba | Provides classes and interfaces for creating Flux Balance Analysis process managers. |
sbrt.shell.mng.geom | Provides classes and for creating geometry process managers. |
sbrt.shell.mng.graph_theory | Provides classes and for creating graph theoretical process managers. |
sbrt.shell.mng.stat | Provides classes and interfaces for creating statistical process managers. |
sbrt.shell.mng.utilities | Provides classes and interfaces for creating mathematical process managers. |
Uses of ManagerInput in plug_in_example.shell |
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Methods in plug_in_example.shell with parameters of type ManagerInput | |
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void |
GreetingManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
Uses of ManagerInput in sbrt |
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Methods in sbrt with parameters of type ManagerInput | |
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void |
ProcessRunner.run(ManagerInput<java.lang.String,java.lang.String> processInput,
java.io.OutputStream out)
Executes the process specified in the provided process manager input. |
void |
ProcessRunner.run(ManagerInput<java.lang.String,java.lang.String> processInput,
java.io.PrintStream out)
Executes the process specified in the provided process manager input. |
void |
ProcessRunner.run(ManagerInput<java.lang.String,java.lang.String> processInput,
java.io.PrintWriter out)
Executes the process specified in the provided process manager input. |
Uses of ManagerInput in sbrt.shell |
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Methods in sbrt.shell with parameters of type ManagerInput | ||
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static ProcessManager<java.lang.String,java.lang.String> |
ProcessManagerFactory.make(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Prints a formatted string representation of the provided input to the provided print writer and returns its corresponding process manager. |
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static
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ProgramSolverFactory.make(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the information contained in the provided input to create a new program solver object. |
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static void |
ProcessManagerFactory.printInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Creates a formatted string representation of the provided input and prints it to the provided print writer. |
Uses of ManagerInput in sbrt.shell.io |
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Classes in sbrt.shell.io that implement ManagerInput | |
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class |
ProcessInputFile
This class is used to represent process input files. |
Uses of ManagerInput in sbrt.shell.mng |
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Classes in sbrt.shell.mng that implement ManagerInput | |
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class |
MapManagerInput<K,V>
This class is a concrete implemenation of ManagerInput. |
Methods in sbrt.shell.mng with parameters of type ManagerInput | |
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void |
ProcessManager.check(ManagerInput<K,V> input)
Throws an ApplicationException if this ProcessManager
cannot understand the provided input. |
void |
AbstractProcessManager.check(ManagerInput<java.lang.String,java.lang.String> input)
Throws an ApplicationException if this ProcessManager cannot
understand the provided input. |
static FileFormat |
AbstractProcessManager.getFileFormat(ManagerInput<java.lang.String,java.lang.String> input)
Returns the parsed value for AbstractProcessManager.FILE_FORMAT in the provided input. |
static TextInputFile<java.lang.String> |
AbstractProcessManager.getFileNameSource(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the parsed value for AbstractProcessManager.OUTPUT_FILE_NAME_FILE in the provided input and prints a descriptive message to the provided print writer. |
static int |
AbstractProcessManager.getIterations(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the parsed value for AbstractProcessManager.ITERATIONS in the provided input and prints a descriptive message to the provided print writer. |
static long |
AbstractProcessManager.getSeed(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the parsed value for AbstractProcessManager.SEED in the provided input and prints a descriptive message to the provided print writer. |
static FileFormat |
AbstractProcessManager.getTextFileFormat(ManagerInput<java.lang.String,java.lang.String> input)
Returns the parsed value for AbstractProcessManager.FILE_FORMAT in the provided input. |
static double |
AbstractProcessManager.getZeroCutoff(ManagerInput<java.lang.String,java.lang.String> input)
Returns the parsed value for AbstractProcessManager.ZERO_CUTOFF in the provided input. |
static double |
AbstractProcessManager.getZeroCutoff(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the parsed value for AbstractProcessManager.ZERO_CUTOFF in the provided input. |
void |
ProcessManager.setInput(ManagerInput<K,V> input)
Uses the provided input to prepare this process manager for execution. |
void |
ProcessManager.setInput(ManagerInput<K,V> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
AbstractProcessManager.setInput(ManagerInput<java.lang.String,java.lang.String> input)
Uses the provided input to prepare this process manager for execution. |
Uses of ManagerInput in sbrt.shell.mng.algebra |
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Methods in sbrt.shell.mng.algebra with parameters of type ManagerInput | |
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static java.util.Map<LinearComb<java.lang.String>,java.lang.Double> |
LinearSolverManager.getEquations(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the set of linear equations contained in the file with the provided name. |
static MathematicaSolver<java.lang.String> |
LinearSolverManager.getSolver(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the linear system solver specified by LinearSolverManager.KERNEL_LINK_CMD in the provided input. |
void |
LinearSolverManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
MultipleVectorsConverterManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
MatrixConverterManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
LinearCombConverterManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
SingleVectorConverterManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
Uses of ManagerInput in sbrt.shell.mng.comb |
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Methods in sbrt.shell.mng.comb with parameters of type ManagerInput | |
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static OutputFile<java.util.Set<java.lang.String>> |
SingleElementUnionManager.getOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns an output file with the name provided in the manager input. |
static java.util.List<java.util.Set<java.lang.String>> |
SingleElementUnionManager.getSets(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the list of sets contained in the file with the name contained in the provided input. |
void |
StrictSingleElementUnionManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
SingleElementUnionManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
Uses of ManagerInput in sbrt.shell.mng.fba |
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Methods in sbrt.shell.mng.fba with parameters of type ManagerInput | ||
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static ExtremeCurrentComputer |
ExtremeCurrentManager.getComputer(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns an extreme current computer created from the provided input. |
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static ReverseRxnIntervalComp<IrrevRxnFluxome> |
ReverseRxnFluxIntervalManager.getComputer(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the flux interval computer specified by the provided input. |
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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. |
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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. |
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static double |
FbaManager.getConstraintTolerance(ManagerInput<java.lang.String,java.lang.String> input)
Parses and returns the value for FbaManager.CONSTRAINT_TOLERANCE in the provided manager input. |
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static double |
FbaManager.getConstraintTolerance(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Parses and returns the value for FbaManager.CONSTRAINT_TOLERANCE in the provided manager input. |
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static FluxIntervalInputFile |
IntervalVariationManager.getCvInputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Returns the constraint variation input with the name denoted by IntervalVariationManager.CV_FILE in the provided manager input. |
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static java.util.List<LinearComb<java.lang.String>> |
FluxCapManager.getCycles(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Opens the file denoted by FluxCapManager.CYCLE_FILE in the provided manager input and returns the list of cycles it contains. |
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static java.util.Set<java.lang.String> |
FbaOptManager.getDataHeaders(ManagerInput<java.lang.String,java.lang.String> input,
Fluxome fluxome)
Parses and returns the value for AbstractProcessManager.DATA_HEADERS in the provided manager input. |
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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. |
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static UnmodifiableMap<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> |
MsFluxIntervalManager.getFluxCaps(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns the flux caps contained in the file with the name specified by MsFluxIntervalManager.FLUX_CAP_FILE in the provided input. |
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static MapInputFile<java.lang.String,Interval> |
FluxPlasticityManager.getFluxIntervalFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns the flux interval input with the name denoted by FluxPlasticityManager.FLUX_INTERVAL_FILE in the provided manager input. |
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static LinearSystemSolution<java.lang.String> |
FbaManager.getFluxomeSolution(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double coeffCutoff)
Opens the file denoted by FbaManager.SYSTEM_SOLUTION_FILE in the provided manager input and returns the linear system solution it contains. |
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static java.util.Map<java.lang.String,java.lang.Double> |
CdHarFluxVectorManager.getFluxVector(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Opens the file denoted by CdHarManager.INITIAL_POINT_FILE in the provided manager input and returns the flux vector it contains. |
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static java.util.Map<java.lang.String,java.lang.Double> |
RandomFluxVectorManager.getFluxVector(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Opens the file denoted by FbaManager.FLUX_VECTOR_FILE in the provided manager input and returns the flux vector it contains. |
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static MapOutputFile<java.lang.String,java.lang.Double> |
InitialPointManager.getFluxVectorFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing a single flux vector. |
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static MapInputFile<java.lang.String,java.lang.Double> |
FluxActivityManager.getFluxVectorFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns the flux vector input file specified by the provided input. |
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static Interval |
RandomConstraintsManager.getInactive(ManagerInput<java.lang.String,java.lang.String> input)
Parses and returns the value for RandomConstraintsManager.INACTIVE in the provided manager input. |
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static InputFile<java.util.Set<java.lang.String>> |
RxnDeletionManager.getInputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Parses and returns the value for RxnDeletionManager.RXN_DELETION_FILE in the provided manager input. |
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static TextInputFile<LinearComb<java.lang.String>> |
ObjectiveFunctionManager.getInputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns the file denoted by ObjectiveFunctionManager.OBJ_FUNCT_FILE in the provided manager input. |
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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. |
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static MsFluxIntervalComputer<IrrevRxnFluxome> |
MsFluxIntervalManager.getIrrevComp(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the flux interval computer specified by the provided input. |
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static Interval |
RandomConstraintsManager.getIrrevConstraint(ManagerInput<java.lang.String,java.lang.String> input)
Parses and returns the value for RandomConstraintsManager.IRREV_CONSTRAINT in the provided manager input. |
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static FbaOptimizer<IrrevRxnFluxome> |
FbaOptManager.getIrrevRxnComp(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Creates and returns an FBA optimization computer based on the provided input. |
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static IrrevRxnFluxome |
FbaOptManager.getIrrevRxnFluxome(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Creates and returns a fluxome based on the provided input. |
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static IrrevRxnFluxome |
FbaManager.getIrrevRxnFluxome(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. |
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static IrrevRxnFluxome |
RandomFluxVectorManager.getIrrevRxnFluxome(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Creates and returns a fluxome based on the provided input. |
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static IrrevRxnFluxome |
FbaOptManager.getIrrevRxnFluxome(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
double tolerance)
Creates and returns a fluxome based on the provided input. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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static
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FbaOptManager.getMultiColOrOutputFiles(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
java.util.Iterator<java.lang.String> fileNameSource,
java.lang.String fileNameSourceName,
F fluxome)
Returns a source of column-oriented FBA optimization output files. |
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static
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FbaOptManager.getMultiFileOutput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
java.util.Iterator<java.lang.String> fileNameSource,
java.lang.String fileNameSourceName,
F fluxome)
Returns a source of FBA optimization output files. |
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static MapOutputFile<java.lang.String,java.lang.Double> |
CdHarFluxVectorManager.getMultiFluxVectorOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple flux vectors. |
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static MapOutputFile<java.lang.String,java.lang.Double> |
FbaManager.getMultiFluxVectorOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple flux vectors. |
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static
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FbaOptManager.getMultiResultsOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
F fluxome)
Returns an empty output file that is suitable for storing multiple FBA optimization results. |
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static ComoFile<java.lang.String,Interval> |
SimpleFluxIntervalManager.getMultiResultsOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple sets of flux interval results. |
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static
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FbaOptManager.getMultiRowOrOutputFiles(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
java.util.Iterator<java.lang.String> fileNameSource,
F fluxome)
Returns a source of row-oriented FBA optimization output files. |
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static
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FbaOptManager.getMultiSerOutputFiles(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
java.util.Iterator<java.lang.String> fileNameSource,
java.lang.String fileNameSourceName,
F fluxome)
Returns a source of serialized FBA optimization output files. |
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static int |
RandomConstraintsManager.getNumActiveFluxes(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Parses and returns the value for RandomConstraintsManager.NUM_ACTIVE_FLUXES in the provided manager input. |
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static LinearComb<java.lang.String> |
FbaOptManager.getObjFunc(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Parses and returns the value for FbaOptManager.OBJECTIVE_FUNCTION in the provided manager input. |
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static OptSense |
FbaOptManager.getOptSense(ManagerInput<java.lang.String,java.lang.String> input)
Parses and returns the value for FbaOptManager.OPTIMIZATION_SENSE in the provided manager input. |
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static MapTextOutputFile<java.lang.String,Interval> |
RandomConstraintsManager.getOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple sets of flux constraints. |
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static TextOutputFile<LinearComb<java.lang.String>> |
RandomObjectiveManager.getOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing randomly generated objective functions. |
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static ComoFile<java.lang.String,java.lang.Double> |
ExtremeCurrentManager.getOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
java.util.Set<java.lang.String> rxnNames)
Returns an output file to which extreme currents can be written. |
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static double |
InitialPointManager.getPIntercept(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the parsed value for InitialPointManager.P_MAX in the provided input. |
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static MapOutputFile<java.lang.String,java.lang.Double> |
InitialPointManager.getPVectorFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing a single C vector with the name denoted by InitialPointManager.P_VECTOR_FILE_NAME in the provided input. |
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static Interval |
RandomConstraintsManager.getRevConstraint(ManagerInput<java.lang.String,java.lang.String> input)
Parses and returns the value for RandomConstraintsManager.REV_CONSTRAINT in the provided manager input. |
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static java.util.Set<java.lang.String> |
FbaManager.getRxnNameHeaders(ManagerInput<java.lang.String,java.lang.String> input,
Fluxome fluxome)
Parses and returns the value for AbstractProcessManager.DATA_HEADERS in the provided manager input. |
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static int |
FbaOptManager.getSafetyLevel(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Parses and returns the value for FbaOptManager.SAFETY_LEVEL in the provided manager input. |
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static MapOutputFile<java.lang.String,java.lang.Double> |
FbaManager.getSingleFluxVectorOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing a single flux vector. |
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static
|
FbaOptManager.getSingleResultOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
F fluxome)
Returns an empty output file that is suitable for storing a single FBA optimization result. |
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static RomoFile<java.lang.String,Interval> |
SimpleFluxIntervalManager.getSingleResultOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing a single set of flux interval results. |
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static FluxIntervalInputFile |
IntervalVariationManager.getSvInputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Returns the space variation input with the name denoted by IntervalVariationManager.FLUX_INTERVAL_FILE in the provided manager input. |
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void |
WwFluxomeReducerManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
|
void |
RandomConstraintsManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
MetatoolInputWriterManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
CdHarFluxVectorManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
ExtremeCurrentManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
CvFbaOptManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
NetworkInfoManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
|
void |
FluxCapManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
ReverseRxnFluxIntervalManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
SimpleFluxIntervalManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
FbaOptManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
RxnDeletionManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
CvRxnDeletionManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
ObjectiveFunctionManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
SlpCycleIdManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
SimpleRxnFileTransManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
RevRxnBreakerManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
MetatoolInputReaderManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
CvCatalystDeletionManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
MetatoolOutputReaderManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
MsFluxomeReducerManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
FbaSolverManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
BiggSbmlReaderManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
CvRevRxnFluxIntervalManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
FluxPlasticityManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
MsFluxIntervalManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
RandomObjectiveManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
CvMsFluxIntervalManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
CvSimpleFluxIntervalManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
CatalystDeletionManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
RedundRxnRemoverManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
InitialPointManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
PalssonSbmlReaderManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
CvObjectiveFunctionManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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void |
FluxActivityManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
Uses of ManagerInput in sbrt.shell.mng.geom |
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Methods in sbrt.shell.mng.geom with parameters of type ManagerInput | |
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static double |
CdHarManager.getConstraintTolerance(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Parses and returns the value for CdHarManager.CONSTRAINT_TOLERANCE in the provided manager input. |
static java.util.Map<java.lang.String,java.lang.Double> |
CdHarManager.getInitialPoint(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
java.util.Set<java.lang.String> variables)
Opens the file with the name denoted by CdHarManager.INITIAL_POINT_FILE and return the vector it contains. |
static int |
CdHarManager.getMaxObstructedMoves(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Parses and returns the value for CdHarManager.MAX_OBSTRUCTED_MOVES in the provided manager input. |
static double |
CdHarManager.getMinChordLength(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Parses and returns the value for CdHarManager.MIN_CHORD_LENGTH in the provided manager input. |
static ComoFile<java.lang.String,java.lang.Double> |
CdHarManager.getOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
java.util.Set<java.lang.String> headers)
Returns an output file with the name provided in the manager input. |
static java.util.Set<ParallelHyperplanes<java.lang.String>> |
CdHarManager.getPlanes(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the list of sets contained in the file with the name contained in the provided input. |
static int |
CdHarManager.getPointsPerPoint(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Parses and returns the value for CdHarManager.POINTS_PER_POINT in the provided manager input. |
void |
CdHarManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
Uses of ManagerInput in sbrt.shell.mng.graph_theory |
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Methods in sbrt.shell.mng.graph_theory with parameters of type ManagerInput | |
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static DirectedGraph<java.lang.String> |
PathIdManager.getGraph(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Opens the file denoted by PathIdManager.EDGE_FILE in the provided manager input and returns the directed graph it contains. |
static TextOutputFile<java.util.List<java.lang.String>> |
CycleIdManager.getOutputFile(ManagerInput<java.lang.String,java.lang.String> input)
Creates a returns an output file if one is specified in the provided input. |
static TextOutputFile<java.util.List<java.lang.String>> |
CycleIdManager.getOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Creates a returns an output file if one is specified in the provided input. |
void |
GraphInfoManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
CycleIdManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
UniqueCycleIdManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
PathIdManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
Uses of ManagerInput in sbrt.shell.mng.stat |
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Methods in sbrt.shell.mng.stat with parameters of type ManagerInput | |
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static UnmodifiableMap<java.lang.String,java.lang.Double> |
CorrelationManager.getXValues(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the parsed value for CorrelationManager.X_FILE_NAME in the provided input and prints a descriptive message to the provided print writer. |
static UnmodifiableMap<java.lang.String,java.lang.Double> |
CorrelationManager.getYValues(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the parsed value for CorrelationManager.Y_FILE_NAME in the provided input and prints a descriptive message to the provided print writer. |
void |
MannWhitneyUManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
KendallTauManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
CorrelationManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
Uses of ManagerInput in sbrt.shell.mng.utilities |
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Methods in sbrt.shell.mng.utilities with parameters of type ManagerInput | |
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static java.util.List<LinearComb<java.lang.String>> |
VariableParticipationManager.getExpressions(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Opens the file denoted by VariableParticipationManager.EXPRESSION_FILE in the provided manager input and returns the list of mathematical expressions it contains. |
void |
VariableParticipationManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
VectorComparisonManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
void |
IntervalComparisonManager.setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
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