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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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