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Packages that use FileFormat | |
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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 | 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 |
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Fields in sbrt.shell.io declared as FileFormat | |
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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 | |
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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 | |
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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 | |
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AbstractMapInputFile(java.lang.String fileName,
FileFormat fileFormat,
MapFormat<K,V> mapFormat)
Constructs a new map input file from the provided arguments. |
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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. |
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AbstractMapOutputFile(java.lang.String fileName,
FileFormat fileFormat,
MapFormat<K,V> mapFormat)
Constructs a new vector output file from the provided arguments. |
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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. |
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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. |
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ComiFile(java.lang.String fileName,
FileFormat fileFormat,
MapFormat<K,V> mapFormat)
Constructs a new row-oriented map input file from the provided arguments. |
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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. |
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ComiFileSource(java.util.Iterator<java.lang.String> fileNameSource,
FileFormat fileFormat,
MapFormat<K,V> mapFormat)
Constructs a new source of column-oriented map input files. |
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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. |
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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. |
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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. |
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ComoFileSource(java.util.Iterator<java.lang.String> fileNameSource,
FileFormat fileFormat,
MapFormat<K,V> mapFormat)
Constructs a new source of column-oriented map output files. |
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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. |
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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. |
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RomiFile(java.lang.String fileName,
FileFormat fileFormat,
MapFormat<K,V> mapFormat)
Constructs a new row-oriented map input file from the provided arguments. |
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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. |
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RomiFileSource(java.util.Iterator<java.lang.String> fileNameSource,
FileFormat fileFormat,
MapFormat<K,V> mapFormat)
Constructs a new source of row-oriented map input files. |
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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. |
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RomoFile(java.lang.String fileName,
FileFormat fileFormat,
MapFormat<K,V> vectorFormat)
Constructs a new row-oriented vector output file from the provided arguments. |
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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. |
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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. |
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RomoFileSource(java.util.Iterator<java.lang.String> fileNameSource,
FileFormat fileFormat,
MapFormat<K,V> mapFormat)
Constructs a new source of row-oriented map output files. |
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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. |
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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. |
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SerializedInputFile(java.lang.String fileName,
FileFormat fileFormat)
Constructs a new text input file using the provided arguments. |
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SerializedMapInputFile(java.lang.String fileName,
FileFormat fileFormat)
Constructs a new input file using the provided arguments. |
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SerializedMapInputFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<? extends K> requiredKeys)
Constructs a new input file using the provided arguments. |
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SerializedOutputFile(java.lang.String fileName,
FileFormat fileFormat)
Constructs a new serialized output file from the provided arguments. |
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SmoFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<? extends K> allKeys)
Constructs a new serialized map output file from the provided arguments. |
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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. |
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TextInputFile(java.lang.String fileName,
FileFormat fileFormat,
Parser<E> fileLineFormat)
Constructs a new text input file using the provided arguments. |
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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. |
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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 |
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Methods in sbrt.shell.io.fba that return FileFormat | |
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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 | |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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RowOrFbaOptOutputFile(java.lang.String fileName,
FileFormat fileFormat,
FbaOptFileLineFormat fbaFormat)
Constructs a new row-oriented FBA optimization output file. |
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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. |
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SerFbaOptOutputFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<java.lang.String> filterKeys,
FbaOptFileLineFormat fbaFormat)
Constructs a new serialized FBA optimization output file. |
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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. |
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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 |
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Methods in sbrt.shell.mng that return FileFormat | |
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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 |
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Methods in sbrt.shell.mng.fba with parameters of type FileFormat | ||
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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. |
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static TextInputFile<LinearComb<java.lang.String>> |
ObjectiveFunctionManager.getInputFile(java.lang.String fileName,
FileFormat format,
Fluxome fluxome)
Returns the input file with the provided name. |
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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. |
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static
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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. |
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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. |
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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. |
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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. |
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static
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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 |
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Methods in sbrt.shell.text that return FileFormat | |
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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 | |
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java.lang.String |
FileFormatFormat.format(FileFormat fileFormat)
Returns a formatted string representation of the provided file format. |
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