Uses of Interface
sbrt.shell.io.InputFile

Packages that use InputFile
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.fba Provides classes and interfaces for creating Flux Balance Analysis process managers. 
sbrt.shell.proc.fba Provides classes for converting FBA-related files of different formats. 
 

Uses of InputFile in sbrt.shell.io
 

Subinterfaces of InputFile in sbrt.shell.io
 interface MapInputFile<K,V>
          This interface is used to represent input files that contain maps.
 interface MapTextInputFile<K,V>
          This interface is used to represent text-based input files that contain maps.
 

Classes in sbrt.shell.io that implement InputFile
 class AbstractMapInputFile<K,V>
          This abstract class is a skeleton implemenation of text-based map input files.
 class ComiFile<K,V>
          This class is used to read column-oriented map input files.
 class ProcessInputFile
          This class is used to represent process input files.
 class RomiFile<K,V>
          This class is used to read row-oriented map input files.
 class SerializedInputFile<E>
          This class is used to read input files containing serialized objects.
 class SerializedMapInputFile<K,V>
          This class is used to read input files containing serialized maps.
 class TextInputFile<E>
          This class is used to read input files containing text.
 

Uses of InputFile in sbrt.shell.io.fba
 

Classes in sbrt.shell.io.fba that implement InputFile
 class FluxCapInputFile
          This class is used to read files containing flux caps.
 class FluxIntervalInputFile
          This class is used to read flux interval input files.
 class RxnNamExprSetInputFile<E extends MathExpr<S>,S>
          This class is used to read files containing a set of reaction name expressions.
 

Uses of InputFile in sbrt.shell.mng.fba
 

Methods in sbrt.shell.mng.fba that return InputFile
static InputFile<java.util.Set<java.lang.String>> CatalystDeletionManager.getDeletionFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, CatalyzedFluxome fluxome)
          Parses and returns the value for CatalystDeletionManager.CATALYST_DELETION_FILE in the provided manager input.
static InputFile<java.util.Set<java.lang.String>> CatalystDeletionManager.getDeletionFile(java.lang.String fileName, CatalyzedFluxome fluxome)
          Returns the catalyst input file with the provided name.
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 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.
 

Uses of InputFile in sbrt.shell.proc.fba
 

Methods in sbrt.shell.proc.fba with parameters of type InputFile
 DoubleMatrix<java.lang.String,java.lang.String> MetatoolOutputReader.getElementaryModes(InputFile<java.lang.String> file, java.util.List<java.lang.String> orderedRxnNames)
          Returns the elementary mode matrix contained in the provided Metatool output file.