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Packages that use MapFormat | |
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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.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 |
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Methods in sbrt.shell.io that return MapFormat | |
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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 | |
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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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ComiFile(java.lang.String fileName,
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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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. |
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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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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. |
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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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RomiFile(java.lang.String fileName,
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,
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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RomiFileSource(java.util.Iterator<java.lang.String> fileNameSource,
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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RomoFile(java.lang.String fileName,
MapFormat<K,V> vectorFormat)
Constructs a new plain text, 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. |
Uses of MapFormat in sbrt.shell.io.fba |
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Methods in sbrt.shell.io.fba that return MapFormat | |
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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 | |
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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. |
Uses of MapFormat in sbrt.shell.mng.fba |
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Methods in sbrt.shell.mng.fba with parameters of type MapFormat | |
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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 |
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Methods in sbrt.shell.mng.geom with parameters of type MapFormat | |
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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 |
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Subinterfaces of MapFormat in sbrt.shell.text | |
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interface |
AppInputFileLineFormat
This interface is used to represent the format of lines in process input files. |
Classes in sbrt.shell.text that implement MapFormat | |
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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 |
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Subinterfaces of MapFormat in sbrt.shell.text.fba | |
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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 | |
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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. |
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