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W
warn(String)
- Method in interface sbrt.kernel.io.
WarningHandler
Processes the provided warning message in an appropriate way.
WarningHandler
- Interface in
sbrt.kernel.io
This interface is used to represent a class of objects that deal with warning messages.
WarningHandlerFactory
- Class in
sbrt.kernel.io
This class is used to provide a default
WarningHandler
.
WarningHandlerFactory()
- Constructor for class sbrt.kernel.io.
WarningHandlerFactory
WhitespaceListFormat
<
E
> - Class in
sbrt.shell.text
This class is used to define a format for whitespace-delimited lists.
WhitespaceListFormat(SimpleFormat<E>)
- Constructor for class sbrt.shell.text.
WhitespaceListFormat
Constructs a new whitespace-delimited list format with the provided element format.
WhitespaceListFormat(Formatter<E>, Parser<E>)
- Constructor for class sbrt.shell.text.
WhitespaceListFormat
Constructs a new whitespace-delimited list format with the provided element format.
WhitespaceSetFormat
<
E
> - Class in
sbrt.shell.text
This class is used to define a format for whitespace-delimited sets.
WhitespaceSetFormat(SimpleFormat<E>)
- Constructor for class sbrt.shell.text.
WhitespaceSetFormat
Constructs a new whitespace-delimited set format with the provided element format.
WhitespaceSetFormat(Formatter<E>, Parser<E>)
- Constructor for class sbrt.shell.text.
WhitespaceSetFormat
Constructs a new whitespace-delimited set format with the provided element format.
widthFormat(String, int)
- Static method in class sbrt.kernel.utilities.
Util
Attemps to format the provided string such that system-dependent newline characters appear no more than
maxWidth
characters apart.
WorkingDirectory
- Class in
sbrt.shell
This class is used to manage the working directory of the SBRT.
WorkingDirectory()
- Constructor for class sbrt.shell.
WorkingDirectory
write(int)
- Method in class sbrt.shell.gui.
TextAreaOutputStream
Writes the specified byte as a character to the javax.swing.JTextArea.
write(int)
- Method in class sbrt.shell.gui.
TextPaneOutputStream
Writes the specified byte as a character to the javax.swing.JTextArea.
writeError(String)
- Method in class sbrt.shell.gui.
SbrtOutputPane
Writes the provided string to this output pane as an error message.
writeFile(IrrevRxnFluxome, OutputFile<String>)
- Method in class sbrt.shell.proc.fba.
MetatoolInputWriter
Writes a metatool input file.
writeFile(MixedFluxome, OutputFile<String>)
- Method in class sbrt.shell.proc.fba.
MetatoolInputWriter
Writes a metatool input file.
writeFluxBounds(String)
- Method in class sbrt.shell.proc.fba.
BiggSbmlReader
Writes the flux bounds contained in the SBML file to a file with the provided name.
writeFluxBounds(String)
- Method in class sbrt.shell.proc.fba.
PalssonSbmlReader
Writes the flux bounds contained in the SBML file to a file with the provided name.
writeFluxome(IrrevRxnFluxome, String)
- Static method in class sbrt.shell.mng.fba.
FbaManager
Writes the provided fluxome to a file with the provided name.
writeFluxome(IrrevRxnFluxome, String, PrintWriter)
- Static method in class sbrt.shell.mng.fba.
FbaManager
Writes the provided fluxome to a file with the provided name.
writeFluxome(MixedFluxome, String)
- Static method in class sbrt.shell.mng.fba.
FbaManager
Writes the provided fluxome to a file with the provided name.
writeFluxome(MixedFluxome, String, PrintWriter)
- Static method in class sbrt.shell.mng.fba.
FbaManager
Writes the provided fluxome to a file with the provided name.
writeFluxVector(String)
- Method in class sbrt.shell.proc.fba.
BiggSbmlReader
Writes the flux vector contained in the SBML file to a file with the provided name.
writeFluxVector(String)
- Method in class sbrt.shell.proc.fba.
PalssonSbmlReader
Writes the flux vector contained in the SBML file to a file with the provided name.
writeGenes(String)
- Method in class sbrt.shell.proc.fba.
BiggSbmlReader
Writes the genes contained in the SBML file to a file with the provided name.
writeGenes(String)
- Method in class sbrt.shell.proc.fba.
PalssonSbmlReader
Writes the genes contained in the SBML file to a file with the provided name.
writeIntersection(String, Map<String, Double>, Map<String, Double>, PrintWriter)
- Static method in class sbrt.shell.mng.stat.
CorrelationManager
Writes the intersection of the provided vectors to a file with the specified name.
writeLine(String)
- Method in class sbrt.shell.io.
AbstractMapOutputFile
Writes the provided string to this file as a line.
writeLine(String)
- Method in class sbrt.shell.io.
TextOutputFile
Writes the provided string to this output file.
writeObject(Object)
- Method in class sbrt.shell.io.
SerializedOutputFile
Serializes the provided object and writes it to this file.
writePlain(String)
- Method in class sbrt.shell.gui.
SbrtOutputPane
Writes the provided string to this output pane as plain text.
writeProblem(String)
- Method in class sbrt.ext.cplex.
CplexSolver
Writes the CPLEX model to a file with the provided name.
writeProteins(String)
- Method in class sbrt.shell.proc.fba.
PalssonSbmlReader
Writes the proteins contained in the SBML file to a file with the provided name.
writeRxns(String)
- Method in class sbrt.shell.proc.fba.
BiggSbmlReader
Writes the reactions contained in the SBML file to a file with the provided name.
writeRxns(String)
- Method in class sbrt.shell.proc.fba.
PalssonSbmlReader
Writes the reactions contained in the SBML file to a file with the provided name.
writeSectionBreak()
- Method in class sbrt.shell.gui.
SbrtOutputPane
Writes a section break to this output pane.
WwFluxomeReducer
- Class in
sbrt.kernel.fba.comp
This class is used to reduce the size of fluxomes for the purpose of identifying the steady state cycles they contain.
WwFluxomeReducer(ProgramSolver<Object, Object>)
- Constructor for class sbrt.kernel.fba.comp.
WwFluxomeReducer
Constructs a fluxome reducer from the provided linear program solver.
WwFluxomeReducerManager
- Class in
sbrt.shell.mng.fba
This class is used to manage the WW fluxome reduction algorithm.
WwFluxomeReducerManager()
- Constructor for class sbrt.shell.mng.fba.
WwFluxomeReducerManager
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