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B

BACK_SLASH - Static variable in class sbrt.shell.text.SpecialChars
\
BiggBracketParserV1 - Class in sbrt.shell.text.fba
This class is used to parse bracketed expressions contained in SBML files from the BiGG Database.
BiggBracketParserV1() - Constructor for class sbrt.shell.text.fba.BiggBracketParserV1
 
BiggRxnNodeParser - Class in sbrt.shell.text.fba
This class is used to make a direct translation from SBML 'reaction' nodes into Systems Biology Research Tool objects.
BiggRxnNodeParser() - Constructor for class sbrt.shell.text.fba.BiggRxnNodeParser
Constructs a new SBML reaction node parser.
BiggSbmlReader - Class in sbrt.shell.proc.fba
This class is used to read SBML files downloaded directly from the BiGG Database.
BiggSbmlReader(String) - Constructor for class sbrt.shell.proc.fba.BiggSbmlReader
Constructs a new SBML file reader.
BiggSbmlReaderManager - Class in sbrt.shell.mng.fba
This class is used to manage the reading of SBML files obtained from the BiGG Database.
BiggSbmlReaderManager() - Constructor for class sbrt.shell.mng.fba.BiggSbmlReaderManager
 
BooleanFormat - Interface in sbrt.shell.text
This interface is used to represent a format for boolean values.
BoolRelFormatV1<E> - Class in sbrt.shell.text
This interface is used to represent boolean relationship formats.
BoolRelFormatV1(SimpleFormat<E>) - Constructor for class sbrt.shell.text.BoolRelFormatV1
Constructs a new boolean relation format object that uses the provided format for its elements.
BoundedIntervalFormatV1 - Class in sbrt.shell.text.math
This class is a concrete implementation of IntervalFormat.
BoundedIntervalFormatV1() - Constructor for class sbrt.shell.text.math.BoundedIntervalFormatV1
Constructs a new interval format.
breakPoint() - Method in class sbrt.kernel.io.AbstractResultsManager
Does nothing.
breakPoint() - Method in interface sbrt.kernel.io.ResultsManager
Signals to this manager that a point of discontinuity or change has been reached.
breakPoint() - Method in class sbrt.shell.io.AbstractMapOutputFile
Writes a line of # symbols to this file.
breakPoint() - Method in class sbrt.shell.io.fba.ColumnOrFbaOptOutputFile
Writes a line of # symbols to this file.
breakPoint() - Method in class sbrt.shell.io.fba.RowOrFbaOptOutputFile
Writes a line of # symbols to this file.
breakPoint() - Method in class sbrt.shell.io.fba.SerFbaOptOutputFile
Does nothing.
breakPoint() - Method in class sbrt.shell.io.MultiOutputFiles
Closes the current file if one exists.
breakPoint() - Method in class sbrt.shell.io.SerializedOutputFile
Does nothing.
breakPoint() - Method in class sbrt.shell.io.TextOutputFile
Writes a line of # symbols to this file.
breakRxn(String, RevRxn) - Method in class sbrt.kernel.fba.proc.RevRxnBreakerProcess
Breaks a reversible reaction into a pair of irreversible reactions.
breakRxn(String, RevExchRxn) - Method in class sbrt.kernel.fba.proc.RevRxnBreakerProcess
Breaks a reversible exchange reaction into a pair of irreversible source and sink exchange reactions.
breakRxns(Map<String, ChemRxn>) - Method in class sbrt.kernel.fba.proc.RevRxnBreakerProcess
Breaks reversible reactions into pairs of irreversible reactions.

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