Uses of Interface
sbrt.kernel.fba.Fluxome

Packages that use Fluxome
sbrt.kernel.fba Provides classes and interfaces for creating objects relevant to Flux Balance Analysis. 
sbrt.kernel.fba.comp Provides classes and interfaces for performing Flux Balance Analysis computations. 
sbrt.kernel.fba.proc Provides classes and interfaces for executing Flux Balance Analysis processes. 
sbrt.shell.io.fba Provides classes and interfaces for reading and writing files relevant to Flux Balance Analysis. 
sbrt.shell.mng.fba Provides classes and interfaces for creating Flux Balance Analysis process managers. 
sbrt.shell.text.fba Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis. 
 

Uses of Fluxome in sbrt.kernel.fba
 

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

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

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

Uses of Fluxome in sbrt.kernel.fba.comp
 

Classes in sbrt.kernel.fba.comp with type parameters of type Fluxome
 class AbstractCvComputer<F extends Fluxome>
          This abstract class is a skeleton implementation of FluxCvComputer.
 class AbstractFluxIntervalComputer<F extends Fluxome>
          This abstract class is a skeleton implemenation of FluxIntervalComputer.
 class CdHarFluxComp<F extends Fluxome>
          This class is used to compute randomly distributed vectors within flux space.
 interface CycleComputer<F extends Fluxome>
          This interface is used to represent algorithms for identifying steady state cycles in stoichiometric networks.
 class FbaOptimizer<F extends Fluxome>
          This class is the workhorse of all Flux Balance Analysis optimizations.
 interface FluxCvComputer<F extends Fluxome>
          This interface is used to represent a flux constraint variation computer.
 interface FluxIntervalComputer<F extends Fluxome>
          This interface is used to represent flux interval computers.
 interface FluxomeReducer<T extends Fluxome>
          This interface is used to represent algorithms that reduce the size of fluxomes.
 class InitialPointComputer<F extends Fluxome>
          This class is used to compute initial points for coordinate-direction hit-and-run random flux vector algorithms.
 class RxnDeletionComputer<F extends Fluxome>
          This class is used to compute the effect of deleting reactions in a fluxome.
 class SimpleFluxIntervalComputer<F extends Fluxome>
          This class is used to compute flux intervals in the simplest possible way.
 

Methods in sbrt.kernel.fba.comp with parameters of type Fluxome
static java.util.Collection<java.util.Set<java.lang.String>> RedundRxnRemover.getEquivRxns(Fluxome fluxome)
          Returns the equivalent reactions contained in the provided fluxome.
static LinearSystemSolution<java.lang.String> FbaSolver.solve(Fluxome fluxome, LinearSystemSolver<java.lang.String> solver)
          Solves Sv = 0, where S is the stoichiometry matrix of the provided fluxome and v is the vector of fluxes.
 

Uses of Fluxome in sbrt.kernel.fba.proc
 

Classes in sbrt.kernel.fba.proc with type parameters of type Fluxome
 class AbstractCvFbaOptProcess<F extends Fluxome,R>
          This class is used to represent constraint-variation Flux Balance Analysis processes.
 class CdHarFluxVectorProcess<F extends Fluxome>
          This class is used to perform coordinate direction hit-and-run flux vector processes.
 class CvFbaOptProcess<F extends Fluxome>
          This class is used to perform constraint-variation FBA optimization processes.
 class CvFluxIntervalProcess<F extends Fluxome>
          This class is used to perform constraint variation flux interval processes.
 class CvObjectiveFunctionProcess<F extends Fluxome>
          This class is used to perform constraint-variation objective function processes.
 class CvRxnDeletionProcess<F extends Fluxome>
          This class is used to perform constraint-variation reaction deletion processes.
 class CycleIdProcess<F extends Fluxome>
          This class is used to execute steady state cycle identification processes.
 class FbaOptProcess<F extends Fluxome>
          This class is used to perform a basic Flux Balance Analysis optimization.
 class FbaProcess<F extends Fluxome,R>
          This abstract class is used to represent Flux Balance Analysis processes.
 class FbaSolverProcess<F extends Fluxome>
          This class is used to solve the equation Sv = 0.
 class FluxActivityProcess<F extends Fluxome>
          This class is used to analyze the activity of fluxes.
 class FluxIntervalProcess<F extends Fluxome>
          This class is used to perform flux interval computations.
 class FluxomeReducerProcess<T extends Fluxome>
          This class is used to execute fluxome reduction processes.
 class FluxPlasticityProcess<F extends Fluxome>
          This class is used to analyze the plasticity of fluxes.
 class InitialPointGenerator<F extends Fluxome>
          This class is used to execute initial point generators.
 class ObjFunAnalysis<F extends Fluxome>
          This class is used to perform objective function analyses.
 class RandConstGeneratorV1<F extends Fluxome>
          This class is used to generate random flux constraints.
 class RandomObjectiveGenerator<F extends Fluxome>
          This class is used to generate random objective functions.
 class RxnDeletionProcess<F extends Fluxome>
          This class is used to perform reaction deletion processes.
 class SvCdHarFluxVectorProcess<F extends Fluxome>
          This class is used to perform space variation coordinate direction hit-and-run flux vector processes.
 class SvInitialPointProcess<F extends Fluxome>
          This class is used to perform flux space variation initial point processes.
 

Methods in sbrt.kernel.fba.proc that return Fluxome
 Fluxome RedundRxnRemoverProcess.getFluxome()
          Returns the fluxome for which redundant reactions are to be removed.
 

Method parameters in sbrt.kernel.fba.proc with type arguments of type Fluxome
 void RedundRxnRemoverProcess.run(ResultsManager<Fluxome> resultsManager)
          Adds the information gathered about the fluxome to the provided results manager.
 

Uses of Fluxome in sbrt.shell.io.fba
 

Classes in sbrt.shell.io.fba with type parameters of type Fluxome
 class CofoofSource<F extends Fluxome>
          This class is used to provide a source of column-oriented FBA optimization output files.
 class ColumnOrFbaOptOutputFile<F extends Fluxome>
          This class is used to write column-oriented output files containing FBA optimization data.
 interface FbaOptOutputFile<F extends Fluxome>
          This interface is used to represent FBA optimization output files.
 class RofoofSource<F extends Fluxome>
          This class is used to provide a source of row-oriented FBA optimization output files.
 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.
 class SfoofSource<F extends Fluxome>
          This class is used to provide a source of serialized FBA optimization output files.
 

Methods in sbrt.shell.io.fba that return Fluxome
 Fluxome FluxCapInputFile.getFluxome()
          Returns the fluxome used to verify reaction names.
 

Methods in sbrt.shell.io.fba with parameters of type Fluxome
static FluxConstraints FluxIntervalInputFile.convertConstraints(java.util.Map<LinearComb<java.lang.String>,Interval> intervals, Fluxome fluxome, double tolerance)
          Converts the provided intervals into a FluxConstraints object.
static void FluxIntervalInputFile.verifyFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConsts, Fluxome fluxome, double tolerance)
          Verifies that the provided constraints are legitimate for the provided fluxome.
 

Constructors in sbrt.shell.io.fba with parameters of type Fluxome
FluxIntervalInputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<LinearComb<java.lang.String>> requiredVariables, MapFormat<LinearComb<java.lang.String>,Interval> mapFormat, Fluxome fluxome, double tolerance)
          Constructs a new flux-interval input file.
 

Uses of Fluxome in sbrt.shell.mng.fba
 

Methods in sbrt.shell.mng.fba with type parameters of type Fluxome
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
<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
<F extends Fluxome>
FbaOptOutputFile<F>
FbaOptManager.getMultiResultsOutputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<java.lang.String> dataHeaders, F fluxome)
          Returns an empty output file that is suitable for storing multiple FBA optimization 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
<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
<F extends Fluxome>
FbaOptOutputFile<F>
FbaOptManager.getSingleResultOutputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<java.lang.String> dataHeaders, F fluxome)
          Returns an empty output file that is suitable for storing a single FBA optimization result.
 

Methods in sbrt.shell.mng.fba with parameters of type Fluxome
static java.util.Map<java.lang.String,Or<And<java.lang.String>>> FbaManager.getCatalysts(Fluxome fluxome, java.lang.String fileName)
          Returns the reaction-catalyst associations contained in the file with the provided name.
static java.util.Map<java.lang.String,Or<And<java.lang.String>>> FbaManager.getCatalysts(Fluxome fluxome, java.lang.String fileName, java.io.PrintWriter out)
          Returns the reaction-catalyst associations contained in the file with the provided name.
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 FluxConstraints FbaOptManager.getConstraints(java.lang.String fileName, Fluxome fluxome, double tolerance)
          Returns the set of constraints contained in the file with the provided name.
static FluxConstraints RandomFluxVectorManager.getConstraints(java.lang.String fileName, Fluxome fluxome, double tolerance)
          Returns the set of constraints contained in the file with the provided name.
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 FluxIntervalInputFile IntervalVariationManager.getCvInputFile(java.lang.String fileName, Fluxome fluxome, double tolerance)
          Returns the constraint variation input file with the provided name.
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 java.util.LinkedHashSet<java.lang.String> FbaOptManager.getDataHeaders(java.lang.String dataHeaders, Fluxome fluxome)
          Parses the provided data header string and returns the corresponding set.
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 MapInputFile<java.lang.String,Interval> FluxPlasticityManager.getFluxIntervalFile(java.lang.String fileName, Fluxome fluxome)
          Returns the flux interval input file with the provided name.
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 java.util.Map<java.lang.String,java.lang.Double> RandomFluxVectorManager.getFluxVector(java.lang.String fileName, Fluxome fluxome, double tolerance)
          Returns the flux vector contained in the file with the provided name.
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 MapInputFile<java.lang.String,java.lang.Double> FluxActivityManager.getFluxVectorFile(java.lang.String fileName, FileFormat format, Fluxome fluxome)
          Returns the flux vector input file with the provided name.
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 TextInputFile<LinearComb<java.lang.String>> ObjectiveFunctionManager.getInputFile(java.lang.String fileName, FileFormat format, Fluxome fluxome)
          Returns the input file with the provided name.
static InputFile<java.util.Set<java.lang.String>> RxnDeletionManager.getInputFile(java.lang.String fileName, Fluxome fluxome)
          Returns the reaction name input file with the provided name.
static TextInputFile<LinearComb<java.lang.String>> ObjectiveFunctionManager.getInputFile(java.lang.String fileName, Fluxome fluxome)
          Returns the input file with the provided name.
static FluxIntervalInputFile IntervalVariationManager.getIntervalInputFile(java.lang.String fileName, Fluxome fluxome, double tolerance)
          Returns the flux interval input file with the provided name.
static FluxIntervalInputFile IntervalVariationManager.getIntervalInputFile(java.lang.String fileName, Fluxome fluxome, MapFormat<LinearComb<java.lang.String>,Interval> mapFormat, double tolerance)
          Returns the flux interval input file with the provided name.
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 FluxConstraints InitialPointManager.getIntervals(java.lang.String fileName, Fluxome fluxome, double tolerance)
          Returns the set of flux intervals contained in the file with the provided name.
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 MapOutputFile<java.lang.String,java.lang.Double> FbaManager.getMultiFluxVectorOutputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<java.lang.String> rxnNameHeaders, Fluxome fluxome)
          Returns an empty output file that is suitable for storing multiple flux vectors.
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 ComoFile<java.lang.String,Interval> SimpleFluxIntervalManager.getMultiResultsOutputFile(java.lang.String fileName, java.util.Set<java.lang.String> headers, Fluxome fluxome)
          Returns an empty output file that is suitable for storing multiple sets of flux interval results.
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 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 TextOutputFile<LinearComb<java.lang.String>> RandomObjectiveManager.getOutputFile(java.lang.String fileName, FileFormat format, java.io.PrintWriter out, Fluxome fluxome)
          Returns an empty output file that is suitable for storing randomly generated objective functions.
static MapTextOutputFile<java.lang.String,Interval> RandomConstraintsManager.getOutputFile(java.lang.String fileName, FileFormat format, java.util.Set<java.lang.String> headers, Fluxome fluxome)
          Returns an empty output file that is suitable for storing multiple sets of flux constraints.
static ComoFile<java.lang.String,java.lang.Double> ExtremeCurrentManager.getOutputFile(java.lang.String fileName, 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 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 RxnNameExprFormat<LinearComb<java.lang.String>,java.lang.String> FbaManager.getRxnNameExprFormat(Fluxome f)
          Returns the default reaction name expression format.
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 java.util.LinkedHashSet<java.lang.String> FbaManager.getRxnNameHeaders(java.lang.String dataHeaders, Fluxome fluxome)
          Parses and returns the set of reaction names contained in the provided string.
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 MapOutputFile<java.lang.String,java.lang.Double> FbaManager.getSingleFluxVectorOutputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<java.lang.String> rxnNameHeaders, Fluxome fluxome)
          Returns an empty output file that is suitable for storing a single flux vector.
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 RomoFile<java.lang.String,Interval> SimpleFluxIntervalManager.getSingleResultOutputFile(java.lang.String fileName, java.util.Set<java.lang.String> headers, 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.
static void FbaManager.printFluxomeInfo(Fluxome fluxome, java.io.PrintWriter out)
          Prints basic information about the provided fluxome.
 

Uses of Fluxome in sbrt.shell.text.fba
 

Methods in sbrt.shell.text.fba that return Fluxome
 Fluxome FluxCapFormatV1.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome CatalystSetFormat.getFluxome()
          Returns the fluxome used to verify enzyme names.
 Fluxome ConstraintsFileLineFormatV1.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome FluxVectorFormatV1.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome RxnNameExprFormat.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome ChemSpeciesVerifier.getFluxome()
          Returns the fluxome used to create this chemical species verifier.
 Fluxome RxnNameExprFormatV1.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome FluxVectorFormat.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome RxnNameOrExprFormatV1.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome FbaOptHeaderParserV1.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome RxnNameOrExprFormat.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome FbaOptHeaderFormatter.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome RxnNameSetFormat.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome ConstraintsFileLineFormatV2.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome RxnNameListFormatV1.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome FbaOptHeaderFormatterV1.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome FbaOptHeaderParser.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome FluxomeSolFileLineFormatV1.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome RxnNameVerifier.getFluxome()
          Returns the fluxome used to create this reaction name checker.
 Fluxome RxnNameSetFormatV1.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome RxnNameListFormat.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome FluxomeSolutionFileLineFormat.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome FluxCapFormat.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome FbaOptFileLineFormatV1.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome ConstraintsFileLineFormat.getFluxome()
          Returns the fluxome used to verify reaction names.
 Fluxome FbaOptFileLineFormat.getFluxome()
          Returns the fluxome used to verify reaction names.
 

Constructors in sbrt.shell.text.fba with parameters of type Fluxome
ChemSpeciesVerifier(Fluxome fluxome)
          Constructs a new chemical species verifier for the provided fluxome.
ConstraintsFileLineFormatV1(Fluxome fluxome)
          Constructs a new contraints file line format.
ConstraintsFileLineFormatV2(Fluxome fluxome)
          Constructs a new contraints file line format.
FbaOptFileLineFormatV1(Fluxome fluxome)
          Constructs a new FBA optimization file line format.
FbaOptHeaderFormatterV1(Fluxome fluxome)
          Constructs a new FBA optimization header formatter.
FbaOptHeaderParserV1(Fluxome fluxome)
          Constructs a new FBA optimization header parser.
FluxCapFormatV1(Fluxome fluxome)
          Constructs a new flux cap file line format using the provided fluxome.
FluxomeSolFileLineFormatV1(Fluxome fluxome)
          Constructs a new fluxome solution file line format.
FluxomeSolFileLineFormatV1(Fluxome fluxome, double coeffCutoff)
          Constructs a new fluxome solution file line format.
FluxVectorFormatV1(Fluxome fluxome)
          Constructs a new flux vector format.
RxnNameExprFormatV1(Fluxome fluxome)
          Constructs a new reaction name expression format using the provided fluxome.
RxnNameExprFormatV1(Fluxome fluxome, double coeffCutoff)
          Constructs a new reaction name expression format using the provided fluxome.
RxnNameListFormatV1(Fluxome fluxome)
          Constructs a new reaction name list format using the provided fluxome.
RxnNameOrExprFormatV1(Fluxome fluxome)
          Constructs a new reaction name and expression format.
RxnNameSetFormatV1(Fluxome fluxome)
          Constructs a new reaction name collection format using the provided fluxome.
RxnNameVerifier(Fluxome fluxome)
          Constructs a new reaction name checker for the provided fluxome.