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Packages that use InputFile | |
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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 |
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Subinterfaces of InputFile in sbrt.shell.io | |
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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 | |
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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 |
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Classes in sbrt.shell.io.fba that implement InputFile | |
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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 |
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Methods in sbrt.shell.mng.fba that return InputFile | |
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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. |
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 |
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Methods in sbrt.shell.proc.fba with parameters of type InputFile | |
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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. |
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