Uses of Interface
sbrt.shell.mng.ManagerInput

Packages that use ManagerInput
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
 

Methods in plug_in_example.shell with parameters of type ManagerInput
 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
 

Methods in sbrt with parameters of type ManagerInput
 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
 

Methods in sbrt.shell with parameters of type ManagerInput
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.
static
<R,C> ProgramSolver<R,C>
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.
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
 

Classes in sbrt.shell.io that implement ManagerInput
 class ProcessInputFile
          This class is used to represent process input files.
 

Uses of ManagerInput in sbrt.shell.mng
 

Classes in sbrt.shell.mng that implement ManagerInput
 class MapManagerInput<K,V>
          This class is a concrete implemenation of ManagerInput.
 

Methods in sbrt.shell.mng with parameters of type ManagerInput
 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
 

Methods in sbrt.shell.mng.algebra with parameters of type ManagerInput
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
 

Methods in sbrt.shell.mng.comb with parameters of type ManagerInput
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
 

Methods in sbrt.shell.mng.fba with parameters of type ManagerInput
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.
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.
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 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.
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.
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.
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.
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.
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 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
static
<F extends Fluxome>
MultiOutputFiles<ColumnOrFbaOptOutputFile<F>,FbaOptimizer.Results>
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.
static
<F extends Fluxome>
MultiOutputFiles<? extends FbaOptOutputFile<F>,FbaOptimizer.Results>
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.
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.
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.
static
<F extends Fluxome>
FbaOptOutputFile<F>
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.
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.
static
<F extends Fluxome>
MultiOutputFiles<RowOrFbaOptOutputFile<F>,FbaOptimizer.Results>
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.
static
<F extends Fluxome>
MultiOutputFiles<SerFbaOptOutputFile<F>,FbaOptimizer.Results>
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
static
<F extends Fluxome>
FbaOptOutputFile<F>
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.
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.
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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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
 

Methods in sbrt.shell.mng.geom with parameters of type ManagerInput
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
 

Methods in sbrt.shell.mng.graph_theory with parameters of type ManagerInput
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
 

Methods in sbrt.shell.mng.stat with parameters of type ManagerInput
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
 

Methods in sbrt.shell.mng.utilities with parameters of type ManagerInput
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.