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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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