Uses of Interface
sbrt.kernel.io.ResultsManager

Packages that use ResultsManager
plug_in_example.kernel   
sbrt.kernel Provides interfaces to define processes. 
sbrt.kernel.fba.proc Provides classes and interfaces for executing Flux Balance Analysis processes. 
sbrt.kernel.io Provides classes and interfaces used to perform kernel-level I/O. 
sbrt.kernel.math.algebra.proc Provides classes and interfaces for executing algebra-related processes. 
sbrt.kernel.math.comb.proc Provides classes and interfaces for performing combinatorial analysis-related processes. 
sbrt.kernel.math.geom.proc Provides classes and interfaces for performing geometry-related processes. 
sbrt.kernel.math.graph_theory.proc Provides classes and interfaces for performing graph theoretical processes. 
sbrt.kernel.math.stat.proc Provides classes and interfaces for performing statistical processes. 
sbrt.kernel.utilities.proc Provides classes and interfaces for performing utility processes. 
sbrt.shell.io Provides classes and interfaces for reading and writing files. 
sbrt.shell.io.fba Provides classes and interfaces for reading and writing files relevant to Flux Balance Analysis. 
sbrt.shell.mng Provides classes and interfaces for creating process managers. 
sbrt.shell.mng.fba Provides classes and interfaces for creating Flux Balance Analysis process managers. 
 

Uses of ResultsManager in plug_in_example.kernel
 

Methods in plug_in_example.kernel with parameters of type ResultsManager
 void GreetingProcess.run(ResultsManager<java.lang.String> resultsManager)
          Adds a randomly generated greeting to the provided results manager.
 

Uses of ResultsManager in sbrt.kernel
 

Methods in sbrt.kernel with parameters of type ResultsManager
 void KernelProcess.run(ResultsManager<T> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 

Uses of ResultsManager in sbrt.kernel.fba.proc
 

Methods in sbrt.kernel.fba.proc with parameters of type ResultsManager
 void CdHarFluxVectorProcess.run(ResultsManager<CdHarFluxComp.Results> resultsManager)
          Generates the specified number of random flux vectors and adds each to the provided results manager.
 void SvCdHarFluxVectorProcess.run(ResultsManager<CdHarFluxComp.Results> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 void CycleIdProcess.run(ResultsManager<DoubleMatrix<?,java.lang.String>> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 void ExtremeCurrentProcess.run(ResultsManager<DoubleMatrix<?,java.lang.String>> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 void CvFbaOptProcess.run(ResultsManager<FbaOptimizer.Results> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 void CatalystDeletionProcess.run(ResultsManager<FbaOptimizer.Results> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 void RxnDeletionProcess.run(ResultsManager<FbaOptimizer.Results> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 void CvRxnDeletionProcess.run(ResultsManager<FbaOptimizer.Results> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 void FbaOptProcess.run(ResultsManager<FbaOptimizer.Results> resultsManager)
          Computes the optimal value of the current objective function and adds the results to the provided results manager via its addData(Object) method.
 void CvObjectiveFunctionProcess.run(ResultsManager<FbaOptimizer.Results> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 void ObjFunAnalysis.run(ResultsManager<FbaOptimizer.Results> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 void CvCatalystDeletionProcess.run(ResultsManager<FbaOptimizer.Results> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 void FluxActivityProcess.run(ResultsManager<FluxActivityProcess.Results> resultsManager)
          Iterates thru the flux vector source set via setFluxVectorSource(Iterable), counts the number of active and inactive fluxes in each vector, and adds the results of each to the provided results manager.
 void RedundRxnRemoverProcess.run(ResultsManager<Fluxome> resultsManager)
          Adds the information gathered about the fluxome to the provided results manager.
 void FluxPlasticityProcess.run(ResultsManager<FluxPlasticityProcess.Results> resultsManager)
          Iterates thru the flux interval source set via setFluxRangeSource(Iterable), computes the flux plasticity measures, and adds the results of each to the provided results manager.
 void InitialPointGenerator.run(ResultsManager<InitialPointComputer.Results> resultsManager)
          Generates an initial point and adds it to the provided results manager.
 void SvInitialPointProcess.run(ResultsManager<InitialPointComputer.Results> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 void RandomObjectiveGenerator.run(ResultsManager<LinearComb<java.lang.String>> resultsManager)
          Generates random objective functions and adds them to the provided results manager.
 void FbaSolverProcess.run(ResultsManager<LinearSystemSolution<java.lang.String>> resultsManager)
          Solves Sv = 0 and adds the result to the provided manager.
 void RevRxnBreakerProcess.run(ResultsManager<java.util.Map<java.lang.String,ChemRxn>> resultsManager)
          Breaks the reversible reactions supplied to this process and adds the result to the provided manager.
 void FluxIntervalProcess.run(ResultsManager<java.util.Map<java.lang.String,Interval>> resultsManager)
          Computes the flux intervals of the reactions with the current names and adds them to the provided results manager.
 void RandConstGeneratorV1.run(ResultsManager<java.util.Map<java.lang.String,Interval>> resultsManager)
          Generates sets of random flux constraints and adds them to the provided results manager.
 void CvFluxIntervalProcess.run(ResultsManager<java.util.Map<java.lang.String,Interval>> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 void FluxCapProcess.run(ResultsManager<java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>> resultsManager)
          Computes the flux caps and adds the result to the provided manager.
 void NetworkInfoProcess.run(ResultsManager<NetworkInfoProcess.Results<F>> resultsManager)
          Adds the information gathered about the fluxome to the provided results manager.
 void FluxomeReducerProcess.run(ResultsManager<T> resultsManager)
          Runs this process and adds the generated results to the provided results manager via its addData(Object) method.
 

Uses of ResultsManager in sbrt.kernel.io
 

Classes in sbrt.kernel.io that implement ResultsManager
 class AbstractResultsManager<R>
          This class is a skeleton implemenation of ResultsManager.
 class ListResultsManager<R>
          This class is used to store a list of results that can be easily retrieved.
 class SingleRm<R>
          This class is used to store a single result that can be easily retrieved.
 

Uses of ResultsManager in sbrt.kernel.math.algebra.proc
 

Methods in sbrt.kernel.math.algebra.proc with parameters of type ResultsManager
 void LinearSolverProcess.run(ResultsManager<LinearSystemSolution<V>> resultsManager)
          Solves the system of linear equations and adds the solution to the provided results manager.
 void VectorIntersection.run(ResultsManager<java.util.Map<K,V>> resultsManager)
          and adds the results to the provided results manager.
 

Uses of ResultsManager in sbrt.kernel.math.comb.proc
 

Methods in sbrt.kernel.math.comb.proc with parameters of type ResultsManager
 void SingleElementUnionProc.run(ResultsManager<java.util.Set<java.util.Set<E>>> resultsManager)
          Computes the single-element unions of the provided collection of sets, and adds the results to the provided results manager.
 void StrictSingleElementUnionProc.run(ResultsManager<java.util.Set<java.util.Set<E>>> resultsManager)
          Computes the strict single-element unions of the provided collection of sets, and adds the results to the provided results manager.
 

Uses of ResultsManager in sbrt.kernel.math.geom.proc
 

Methods in sbrt.kernel.math.geom.proc with parameters of type ResultsManager
 void CdHarProcess.run(ResultsManager<CdHarComp.Results> resultsManager)
          Adds random points to the provided results manager.
 

Uses of ResultsManager in sbrt.kernel.math.graph_theory.proc
 

Methods in sbrt.kernel.math.graph_theory.proc with parameters of type ResultsManager
 void CycleIdProcess.run(ResultsManager<Path<N>> resultsManager)
          Adds to the provided results manager each identified cycle in the current graph.
 void PathIdProcess.run(ResultsManager<Path<N>> resultsManager)
          Adds to the provided results manager each computed path in the current graph.
 

Uses of ResultsManager in sbrt.kernel.math.stat.proc
 

Methods in sbrt.kernel.math.stat.proc with parameters of type ResultsManager
 void MwUAnalysis.run(ResultsManager<MannWhitneyResults> resultsManager)
          Computes the Mann-Whitney U statistic of the samples A and B, and adds the results to the provided results manager.
 void CorrelationAnalysis.run(ResultsManager<T> resultsManager)
          Computes the correlation statistic between the x and y values, and adds the results to the provided results manager.
 void MultipleCorrelationAnalysis.run(ResultsManager<T> resultsManager)
          Computes the correlation statistic between the x and y values, and adds the results to the provided results manager.
 

Uses of ResultsManager in sbrt.kernel.utilities.proc
 

Methods in sbrt.kernel.utilities.proc with parameters of type ResultsManager
 void VectorComparison.run(ResultsManager<java.util.Map<V,java.lang.Double>> resultsManager)
          Adds to the provided results manager the variables (keys) whose intervals (values) are unequal within the provided tolerance.
 void VariableParticipation.run(ResultsManager<java.util.Map<V,java.util.List<E>>> resultsManager)
          Adds to the provided results manager a map of variables mapped to a list of mathematical expressions in which they participate.
 void IntervalComparison.run(ResultsManager<java.util.Set<IntervalComparer.Diff<V>>> resultsManager)
          Adds to the provided results manager the variables (keys) whose intervals (values) are not considered equivalent.
 

Uses of ResultsManager in sbrt.shell.io
 

Subinterfaces of ResultsManager in sbrt.shell.io
 interface MapOutputFile<K,V>
          This interface is used to represent output files that maps can be written to.
 interface MapTextOutputFile<K,V>
          This interface is used to represent output files that maps can be written to as text.
 interface OutputFile<T>
          This interface is used to represent output files.
 

Classes in sbrt.shell.io that implement ResultsManager
 class AbstractMapOutputFile<K,V>
          This abstract class is a skeleton implementation of MapTextOutputFile.
 class ComoFile<K,V>
          This class is used to write maps to text files in a column-oriented way.
 class MultiOutputFiles<F extends OutputFile<R>,R>
          This class is used to create multiple output files.
 class RomoFile<K,V>
          This class is used to write maps to text files in a row-oriented way.
 class SerializedOutputFile<E>
          This class is used to write serialized objects to output files.
 class SmoFile<K,V>
          This class is used to write serialized maps to output files.
 class TextOutputFile<T>
          This class is used to represent output files containing plain text.
 

Uses of ResultsManager in sbrt.shell.io.fba
 

Subinterfaces of ResultsManager in sbrt.shell.io.fba
 interface FbaOptOutputFile<F extends Fluxome>
          This interface is used to represent FBA optimization output files.
 

Classes in sbrt.shell.io.fba that implement ResultsManager
 class ColumnOrFbaOptOutputFile<F extends Fluxome>
          This class is used to write column-oriented output files containing FBA optimization data.
 class RowOrFbaOptOutputFile<F extends Fluxome>
          This class is used to write row-oriented output files containing FBA optimization data.
 class SerFbaOptOutputFile<F extends Fluxome>
          This class is used to write output files containing FBA optimization data as serialized maps.
 

Uses of ResultsManager in sbrt.shell.mng
 

Methods in sbrt.shell.mng with parameters of type ResultsManager
static void AbstractProcessManager.closeRm(ResultsManager<?> rm, java.io.PrintWriter out)
          Closes the provided file and prints a descriptive message to the provided print writer.
static
<T> void
AbstractProcessManager.runProcess(MonitoredProcess<T> process, ResultsManager<T> resultsManager, java.io.PrintWriter out)
          Runs the provided process using the provided results manager and prints descriptive progress messages to the provided print writer.
 

Uses of ResultsManager in sbrt.shell.mng.fba
 

Classes in sbrt.shell.mng.fba that implement ResultsManager
protected static class ExtremeCurrentManager.Rm