Uses of Class
sbrt.shell.io.FileFormat

Packages that use FileFormat
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. 
sbrt.shell.text Provides classes and interfaces for defining formats for basic objects. 
 

Uses of FileFormat in sbrt.shell.io
 

Fields in sbrt.shell.io declared as FileFormat
static FileFormat FileFormat.GZIP_SER
          Used to denote a file containing serialized objects that has been compressed using the GNU program gzip.
static FileFormat FileFormat.GZIP_TEXT
          Used to denote a plain-text file that has been compressed using the GNU program gzip.
static FileFormat FileFormat.SERIALIZED
          Used to denote a file containing serialized objects.
static FileFormat FileFormat.TEXT
          Used to denote a plain-text file.
 

Methods in sbrt.shell.io that return FileFormat
 FileFormat SerializedOutputFile.getFileFormat()
          Returns the format of this file.
 FileFormat RomoFileSource.getFileFormat()
          Returns the format used to create files of type RomoFile.
 FileFormat ComoFileSource.getFileFormat()
          Returns the format used to create files of type ComoFile.
 FileFormat TextInputFile.getFileFormat()
          Returns the format of this file.
 FileFormat SmoFileSource.getFileFormat()
          Returns the format used to create files of type SmoFile.
 FileFormat RomiFileSource.getFileFormat()
          Returns the format used to create files of type RomiFile.
 FileFormat ComiFileSource.getFileFormat()
          Returns the format used to create files of type ComiFile.
 FileFormat SerializedInputFile.getFileFormat()
          Returns the format of this file.
 

Methods in sbrt.shell.io with parameters of type FileFormat
static TextOutputFile<java.lang.String> TextOutputFile.getBasic(java.lang.String fileName, FileFormat fileFormat)
          Returns a basic text output file with the provided file format.
static TextInputFile<java.lang.String> TextInputFile.getBasic(java.lang.String fileName, FileFormat fileFormat)
          Returns a basic text input file.
static boolean SerializedOutputFile.isValidFormat(FileFormat fileFormat)
          Indicates if the provided file format is valid for a serialized output file.
static boolean TextOutputFile.isValidFormat(FileFormat fileFormat)
          Indicates if the provided file format is valid for a text output file.
static boolean SerializedFileIterator.isValidFormat(FileFormat fileFormat)
          Indicates if the provided file format is valid for this type of file iterator.
static boolean TextFileLineIterator.isValidFormat(FileFormat fileFormat)
          Indicates if the provided file format is valid for this type of file line iterator.
static boolean TextInputFile.isValidFormat(FileFormat fileFormat)
          Indicates if the provided file format is valid for a text input file.
static boolean SerializedInputFile.isValidFormat(FileFormat fileFormat)
          Indicates if the provided file format is valid for a text input file.
 

Constructors in sbrt.shell.io with parameters of type FileFormat
AbstractMapInputFile(java.lang.String fileName, FileFormat fileFormat, MapFormat<K,V> mapFormat)
          Constructs a new map input file from the provided arguments.
AbstractMapInputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<? extends K> requiredKeys, MapFormat<K,V> mapFormat)
          Constructs a new map input file from the provided arguments.
AbstractMapOutputFile(java.lang.String fileName, FileFormat fileFormat, MapFormat<K,V> mapFormat)
          Constructs a new vector output file from the provided arguments.
AbstractMapOutputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<? extends K> keys, MapFormat<K,V> mapFormat)
          Constructs a new map output file from the provided arguments.
AbstractMapOutputFile(java.lang.String fileName, FileFormat fileFormat, java.lang.String allVariables, MapFormat<K,V> mapFormat)
          Constructs a new map output file from the provided arguments.
ComiFile(java.lang.String fileName, FileFormat fileFormat, MapFormat<K,V> mapFormat)
          Constructs a new row-oriented map input file from the provided arguments.
ComiFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<? extends K> requiredKeys, MapFormat<K,V> mapFormat)
          Constructs a new row-oriented map input file from the provided arguments.
ComiFileSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, MapFormat<K,V> mapFormat)
          Constructs a new source of column-oriented map input files.
ComiFileSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, java.util.Set<? extends K> requiredKeys, MapFormat<K,V> mapFormat)
          Constructs a new source of column-oriented map input files.
ComoFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<? extends K> columnHeaderVariables, MapFormat<K,V> vectorFormat)
          Constructs a new column-oriented map output file from the provided arguments.
ComoFile(java.lang.String fileName, FileFormat fileFormat, java.lang.String allColumnHeaderVariables, MapFormat<K,V> vectorFormat)
          Constructs a new column-oriented vector output file from the provided arguments.
ComoFileSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, MapFormat<K,V> mapFormat)
          Constructs a new source of column-oriented map output files.
ComoFileSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, java.util.Set<? extends K> keys, MapFormat<K,V> mapFormat)
          Constructs a new source of column-oriented map output files.
ComoFileSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, java.lang.String keys, MapFormat<K,V> mapFormat)
          Constructs a new source of column-oriented map output files.
RomiFile(java.lang.String fileName, FileFormat fileFormat, MapFormat<K,V> mapFormat)
          Constructs a new row-oriented map input file from the provided arguments.
RomiFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<? extends K> requiredKeys, MapFormat<K,V> mapFormat)
          Constructs a new row-oriented map input file from the provided arguments.
RomiFileSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, MapFormat<K,V> mapFormat)
          Constructs a new source of row-oriented map input files.
RomiFileSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, java.util.Set<? extends K> requiredKeys, MapFormat<K,V> mapFormat)
          Constructs a new source of row-oriented map input files.
RomoFile(java.lang.String fileName, FileFormat fileFormat, MapFormat<K,V> vectorFormat)
          Constructs a new row-oriented vector output file from the provided arguments.
RomoFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<? extends K> rowHeaderVariables, MapFormat<K,V> mapFormat)
          Constructs a new row-oriented map output file from the provided arguments.
RomoFile(java.lang.String fileName, FileFormat fileFormat, java.lang.String allRowHeaderVariables, MapFormat<K,V> vectorFormat)
          Constructs a new row-oriented vector output file from the provided arguments.
RomoFileSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, MapFormat<K,V> mapFormat)
          Constructs a new source of row-oriented map output files.
RomoFileSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, java.util.Set<? extends K> keys, MapFormat<K,V> mapFormat)
          Constructs a new source of row-oriented map output files.
RomoFileSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, java.lang.String keys, MapFormat<K,V> mapFormat)
          Constructs a new source of row-oriented map output files.
SerializedInputFile(java.lang.String fileName, FileFormat fileFormat)
          Constructs a new text input file using the provided arguments.
SerializedMapInputFile(java.lang.String fileName, FileFormat fileFormat)
          Constructs a new input file using the provided arguments.
SerializedMapInputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<? extends K> requiredKeys)
          Constructs a new input file using the provided arguments.
SerializedOutputFile(java.lang.String fileName, FileFormat fileFormat)
          Constructs a new serialized output file from the provided arguments.
SmoFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<? extends K> allKeys)
          Constructs a new serialized map output file from the provided arguments.
SmoFileSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, java.util.Set<? extends K> keys)
          Constructs a new source of serialized map output files.
TextInputFile(java.lang.String fileName, FileFormat fileFormat, Parser<E> fileLineFormat)
          Constructs a new text input file using the provided arguments.
TextInputFile(java.lang.String fileName, FileFormat fileFormat, Parser<E> fileLineFormat, java.util.Collection<java.lang.Character> commentCharacters)
          Constructs a new text input file using the provided arguments.
TextOutputFile(java.lang.String fileName, FileFormat fileFormat, Formatter<T> lineFormat)
          Constructs a new text output file using the provided arguments.
 

Uses of FileFormat in sbrt.shell.io.fba
 

Methods in sbrt.shell.io.fba that return FileFormat
 FileFormat SfoofSource.getFileFormat()
          Returns the file format used to create files of type SerFbaOptOutputFile.
 FileFormat RofoofSource.getFileFormat()
          Returns the file format used to create files of type RowOrFbaOptOutputFile.
 FileFormat CofoofSource.getFileFormat()
          Returns the file format used to create files of type ColumnOrFbaOptOutputFile.
 

Constructors in sbrt.shell.io.fba with parameters of type FileFormat
CofoofSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, java.util.Set<java.lang.String> columnHeaders, FbaOptFileLineFormat fbaFormat)
          Constructs a new source of column-oriented FBA optimization output files.
CofoofSource(java.util.Iterator<java.lang.String> fileNameSource, java.lang.String fileNameSourceName, FileFormat fileFormat, java.util.Set<java.lang.String> columnHeaders, FbaOptFileLineFormat fbaFormat)
          Constructs a new source of column-oriented FBA optimization output files.
ColumnOrFbaOptOutputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<java.lang.String> columnHeaders, FbaOptFileLineFormat fbaFormat)
          Constructs a new column-oriented FBA optimization output file.
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.
RofoofSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, java.util.Set<java.lang.String> rowHeaders, FbaOptFileLineFormat fbaFormat)
          Constructs a new source of row-oriented FBA optimization output files.
RofoofSource(java.util.Iterator<java.lang.String> fileNameSource, java.lang.String fileNameSourceName, FileFormat fileFormat, java.util.Set<java.lang.String> rowHeaders, FbaOptFileLineFormat fbaFormat)
          Constructs a new source of row-oriented FBA optimization output files.
RowOrFbaOptOutputFile(java.lang.String fileName, FileFormat fileFormat, FbaOptFileLineFormat fbaFormat)
          Constructs a new row-oriented FBA optimization output file.
RowOrFbaOptOutputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<java.lang.String> rowHeaders, FbaOptFileLineFormat fbaFormat)
          Constructs a new row-oriented FBA optimization output file.
SerFbaOptOutputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<java.lang.String> filterKeys, FbaOptFileLineFormat fbaFormat)
          Constructs a new serialized FBA optimization output file.
SfoofSource(java.util.Iterator<java.lang.String> fileNameSource, FileFormat fileFormat, java.util.Set<java.lang.String> filterKeys, FbaOptFileLineFormat fbaFormat)
          Constructs a new source of serialized FBA optimization output files.
SfoofSource(java.util.Iterator<java.lang.String> fileNameSource, java.lang.String fileNameSourceName, FileFormat fileFormat, java.util.Set<java.lang.String> filterKeys, FbaOptFileLineFormat fbaFormat)
          Constructs a new source of serialized FBA optimization output files.
 

Uses of FileFormat in sbrt.shell.mng
 

Methods in sbrt.shell.mng that return FileFormat
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 FileFormat AbstractProcessManager.getFileFormat(java.lang.String formatName)
          Parses and returns the file format corresponding to the provided string.
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 FileFormat AbstractProcessManager.getTextFileFormat(java.lang.String fileFormatString)
          Returns the text file format corresponding to the provided string.
 

Uses of FileFormat in sbrt.shell.mng.fba
 

Methods in sbrt.shell.mng.fba with parameters of type FileFormat
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 TextInputFile<LinearComb<java.lang.String>> ObjectiveFunctionManager.getInputFile(java.lang.String fileName, FileFormat format, Fluxome fluxome)
          Returns the input file with the provided name.
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
<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 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 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
<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.
 

Uses of FileFormat in sbrt.shell.text
 

Methods in sbrt.shell.text that return FileFormat
 FileFormat FileFormatFormat.parse(java.lang.String source)
          Parses the provided string and returns its corresponding file format.
 

Methods in sbrt.shell.text with parameters of type FileFormat
 java.lang.String FileFormatFormat.format(FileFormat fileFormat)
          Returns a formatted string representation of the provided file format.