Uses of Interface
sbrt.shell.text.MapFormat

Packages that use MapFormat
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.mng.geom Provides classes and for creating geometry process managers. 
sbrt.shell.text Provides classes and interfaces for defining formats for basic objects. 
sbrt.shell.text.fba Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis. 
 

Uses of MapFormat in sbrt.shell.io
 

Methods in sbrt.shell.io that return MapFormat
 MapFormat<K,V> RomoFileSource.getLineFormat()
          Returns the map format used to create files of type RomoFile.
 MapFormat<K,V> ComoFileSource.getLineFormat()
          Returns the map format used to create files of type ComoFile.
 MapFormat<K,V> RomiFileSource.getLineFormat()
          Returns the map format used to create files of type RomiFile.
 MapFormat<K,V> ComiFileSource.getLineFormat()
          Returns the map format used to create files of type ComiFile.
 MapFormat<K,V> AbstractMapOutputFile.getMapFormat()
          Returns the format used to write lines to this file.
 MapFormat<K,V> AbstractMapInputFile.getMapFormat()
          Returns the map format used to parse this file.
 MapFormat<K,V> MapTextFile.getMapFormat()
          Returns the map format used by this file.
 

Constructors in sbrt.shell.io with parameters of type MapFormat
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.
ComiFile(java.lang.String fileName, 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.
ComiFileSource(java.util.Iterator<java.lang.String> fileNameSource, 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.
ComoFile(java.lang.String fileName, java.util.Set<? extends K> columnHeaderVariables, MapFormat<K,V> vectorFormat)
          Constructs a new text-based column-oriented map 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.
RomiFile(java.lang.String fileName, MapFormat<K,V> mapFormat)
          Constructs a new row-oriented map input file from the provided arguments.
RomiFile(java.lang.String fileName, 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.
RomiFileSource(java.util.Iterator<java.lang.String> fileNameSource, 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.
RomoFile(java.lang.String fileName, MapFormat<K,V> vectorFormat)
          Constructs a new plain text, 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.
 

Uses of MapFormat in sbrt.shell.io.fba
 

Methods in sbrt.shell.io.fba that return MapFormat
 MapFormat<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> FluxCapInputFile.getMapFormat()
          Returns the map format used to parse this file.
 

Constructors in sbrt.shell.io.fba with parameters of type MapFormat
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 MapFormat in sbrt.shell.mng.fba
 

Methods in sbrt.shell.mng.fba with parameters of type MapFormat
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.
 

Uses of MapFormat in sbrt.shell.mng.geom
 

Methods in sbrt.shell.mng.geom with parameters of type MapFormat
static java.util.Map<java.lang.String,java.lang.Double> CdHarManager.getInitialPoint(java.lang.String fileName, MapFormat<java.lang.String,java.lang.Double> format, java.util.Set<java.lang.String> variables)
          Opens the file with the provided name and return the vector it contains.
 

Uses of MapFormat in sbrt.shell.text
 

Subinterfaces of MapFormat in sbrt.shell.text
 interface AppInputFileLineFormat
          This interface is used to represent the format of lines in process input files.
 

Classes in sbrt.shell.text that implement MapFormat
 class AbstractMapFormat<K,V>
          This abstract class is a skeleton implementation of MapFormat.
 class AppInputFileLineFormatVersion1
          This class is a concrete implementation of AppInputFileLineFormat.
 class ColonMapFormatV1<K,V>
          This class is a concrete implementation of MapFormat.
 class EqualsMapFormatV1<K,V>
          This class is a concrete implementation of MapFormat.
 

Uses of MapFormat in sbrt.shell.text.fba
 

Subinterfaces of MapFormat in sbrt.shell.text.fba
 interface ConstraintsFileLineFormat<E>
          This interface is used to represent formats for flux constraints files.
 interface FbaOptFileLineFormat
          This interface is used to represent formats of FBA optimization file lines.
 interface FluxCapFormat
          This interface is used to represent the formats of lines of flux cap-containing files.
 interface FluxomeSolutionFileLineFormat
          This interface is used to represent formats for solutions to the linear system of equations formed by a fluxome.
 interface FluxVectorFormat
          This interface is used to represent formats for flux vectors.
 

Classes in sbrt.shell.text.fba that implement MapFormat
 class ConstraintsFileLineFormatV1
          This class is a concrete implemenation of ConstraintsFileLineFormat.
 class ConstraintsFileLineFormatV2
          This class is a concrete implemenation of ConstraintsFileLineFormat.
 class FbaOptFileLineFormatV1
          This class is a concrete implementation of FbaOptFileLineFormat.
 class FluxCapFormatV1
          This class is a concrete implementation of FluxCapFormat.
 class FluxomeSolFileLineFormatV1
          This class is a concrete implemenation of FluxomeSolutionFileLineFormat.
 class FluxVectorFormatV1
          This class is a concrete implemenation of FluxVectorFormat.
 class IrfFormatV1
          This class is used to format irreversible reaction fluxome files.
 class MixedFluxomeFormatV1
          This class is used to format irreversible reaction fluxome files.