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F
FatalException
- Exception in
sbrt
This class is used to represent an unrecoverable, or fatal, exception.
FatalException(String)
- Constructor for exception sbrt.
FatalException
Constructs a new object.
FbaManager
- Class in
sbrt.shell.mng.fba
This abstract class provides a foundation for Flux Balance Analysis process managers.
FbaManager()
- Constructor for class sbrt.shell.mng.fba.
FbaManager
FbaOptException
- Exception in
sbrt.kernel.fba.comp
This class is used to indicate that an optimal solution could not be found or does not exist.
FbaOptException(MathExpr<?>, OptSense, ProgramSolverStatus)
- Constructor for exception sbrt.kernel.fba.comp.
FbaOptException
Constructs a new FBA optimization exception.
FbaOptException(MathExpr<?>, OptSense, ProgramSolverStatus, String)
- Constructor for exception sbrt.kernel.fba.comp.
FbaOptException
Constructs a new FBA optimization exception.
FbaOptFileLineFormat
- Interface in
sbrt.shell.text.fba
This interface is used to represent formats of FBA optimization file lines.
FbaOptFileLineFormatV1
- Class in
sbrt.shell.text.fba
This class is a concrete implementation of
FbaOptFileLineFormat
.
FbaOptFileLineFormatV1(Fluxome)
- Constructor for class sbrt.shell.text.fba.
FbaOptFileLineFormatV1
Constructs a new FBA optimization file line format.
FbaOptHeaderFormatter
- Interface in
sbrt.shell.text.fba
This interface is used to represent formatters for headers used in writing files of FBA optimization data.
FbaOptHeaderFormatterV1
- Class in
sbrt.shell.text.fba
This class is a concrete implemenation of
FbaOptHeaderFormatter
.
FbaOptHeaderFormatterV1(Fluxome)
- Constructor for class sbrt.shell.text.fba.
FbaOptHeaderFormatterV1
Constructs a new FBA optimization header formatter.
FbaOptHeaderParser
- Interface in
sbrt.shell.text.fba
This interface is used to represent parsers for headers used in writing files of FBA optimization data.
FbaOptHeaderParserV1
- Class in
sbrt.shell.text.fba
This class is a concrete implemenation of
FbaOptHeaderParser
.
FbaOptHeaderParserV1(Fluxome)
- Constructor for class sbrt.shell.text.fba.
FbaOptHeaderParserV1
Constructs a new FBA optimization header parser.
FbaOptimizer
<
F
extends
Fluxome
> - Class in
sbrt.kernel.fba.comp
This class is the workhorse of all Flux Balance Analysis optimizations.
FbaOptimizer(F, ProgramSolver<Object, Object>)
- Constructor for class sbrt.kernel.fba.comp.
FbaOptimizer
Constructs a new FBA optimization computer from the provided fluxome and program solver.
FbaOptimizer(F, ProgramSolver<Object, Object>, double)
- Constructor for class sbrt.kernel.fba.comp.
FbaOptimizer
Constructs a new FBA optimization computer from the provided fluxome, program solver, and constraint tolerance.
FbaOptimizer.Results
- Class in
sbrt.kernel.fba.comp
This class is used to store the results of an FBA optimization problem.
FbaOptManager
- Class in
sbrt.shell.mng.fba
This class is used to manage basic FBA optimization processes.
FbaOptManager()
- Constructor for class sbrt.shell.mng.fba.
FbaOptManager
FbaOptOutputFile
<
F
extends
Fluxome
> - Interface in
sbrt.shell.io.fba
This interface is used to represent FBA optimization output files.
FbaOptProcess
<
F
extends
Fluxome
> - Class in
sbrt.kernel.fba.proc
This class is used to perform a basic Flux Balance Analysis optimization.
FbaOptProcess(FbaOptimizer<F>)
- Constructor for class sbrt.kernel.fba.proc.
FbaOptProcess
Constructs a new FBA optimization process.
FbaProcess
<
F
extends
Fluxome
,
R
> - Class in
sbrt.kernel.fba.proc
This abstract class is used to represent Flux Balance Analysis processes.
FbaProcess()
- Constructor for class sbrt.kernel.fba.proc.
FbaProcess
FbaSolver
- Class in
sbrt.kernel.fba.comp
This class is used to solve the system of linear equations
Sv = 0
.
FbaSolver()
- Constructor for class sbrt.kernel.fba.comp.
FbaSolver
FbaSolverManager
- Class in
sbrt.shell.mng.fba
This class is used to manage FBA solver processes.
FbaSolverManager()
- Constructor for class sbrt.shell.mng.fba.
FbaSolverManager
FbaSolverProcess
<
F
extends
Fluxome
> - Class in
sbrt.kernel.fba.proc
This class is used to solve the equation Sv = 0.
FbaSolverProcess(F)
- Constructor for class sbrt.kernel.fba.proc.
FbaSolverProcess
Constructs a new FBA solver process.
FILE
- Static variable in class sbrt.shell.mng.utilities.
VectorComparisonManager
The string used to indicate the name of the vector file.
FILE_1
- Static variable in class sbrt.shell.mng.utilities.
IntervalComparisonManager
The string used to indicate the name of the first file.
FILE_2
- Static variable in class sbrt.shell.mng.utilities.
IntervalComparisonManager
The string used to indicate the name of the second file.
FILE_FORMAT
- Static variable in class sbrt.shell.mng.
AbstractProcessManager
The keyword used to denote the name of a file format.
FileFormat
- Class in
sbrt.shell.io
This class is used to represent file formats.
FileFormatFormat
- Class in
sbrt.shell.text
This class is used to represent formats for types of file formats.
FileFormatFormat()
- Constructor for class sbrt.shell.text.
FileFormatFormat
FileLineIterator
<
E
> - Class in
sbrt.shell.io
This class is used to iterate through the lines of a file.
FileLineIterator()
- Constructor for class sbrt.shell.io.
FileLineIterator
finalize()
- Method in class sbrt.ext.mma.algebra.
MathematicaSolver
Calls
close()
.
finalize()
- Method in class sbrt.shell.io.
SerializedFileIterator
Disposes of system resources associated with this file iterator when called by the garbage collector.
finalize()
- Method in class sbrt.shell.io.
SerializedInputFile
Disposes of system resources associated with this file when called by the garbage collector.
finalize()
- Method in class sbrt.shell.io.
SerializedOutputFile
Disposes of system resources associated with this file when called by the garbage collector.
finalize()
- Method in class sbrt.shell.io.
TextFileLineIterator
Disposes of system resources associated with this file iterator when called by the garbage collector.
finalize()
- Method in class sbrt.shell.io.
TextInputFile
Disposes of system resources associated with this file when called by the garbage collector.
finalize()
- Method in class sbrt.shell.io.
TextOutputFile
Disposes of system resources associated with this file when called by the garbage collector.
fixedVariables()
- Method in class sbrt.kernel.math.algebra.
HashLinearSystemSolution
Returns the number of fixed variables in this solution.
fixedVariables()
- Method in interface sbrt.kernel.math.algebra.
LinearSystemSolution
Returns the number of fixed variables in this solution.
FLUX_BOUNDS_FILE_NAME
- Static variable in class sbrt.shell.mng.fba.
PalssonSbmlReaderManager
Used to denote the name of the file to which the flux bounds should be written.
FLUX_CAP_FILE
- Static variable in class sbrt.shell.mng.fba.
MsFluxIntervalManager
The keyword used to denote the flux cap input file.
FLUX_INTERVAL_FILE
- Static variable in class sbrt.shell.mng.fba.
FluxPlasticityManager
The keyword used to denote the name of the file containing the sets of flux intervals.
FLUX_INTERVAL_FILE
- Static variable in class sbrt.shell.mng.fba.
InitialPointManager
The keyword used to denote the name of the file containing the set of flux intervals.
FLUX_INTERVAL_FILE
- Static variable in class sbrt.shell.mng.fba.
IntervalVariationManager
The keyword used to denote a flux interval input file.
FLUX_VECTOR_FILE
- Static variable in class sbrt.shell.mng.fba.
FbaManager
The keyword used to denote a flux vector input file.
FLUX_VECTOR_FILE_FORMAT
- Static variable in class sbrt.shell.mng.fba.
FluxActivityManager
The keyword used to denote the format of the flux vector input file.
FLUX_VECTOR_FILE_NAME
- Static variable in class sbrt.shell.mng.fba.
FbaManager
The keyword used to denote the name of a flux vector output file.
FLUX_VECTOR_FILE_NAME
- Static variable in class sbrt.shell.mng.fba.
PalssonSbmlReaderManager
Used to denote the name of the file to which the flux vector should be written.
FluxActivityManager
- Class in
sbrt.shell.mng.fba
This class is used to manage flux activity processes.
FluxActivityManager()
- Constructor for class sbrt.shell.mng.fba.
FluxActivityManager
FluxActivityProcess
<
F
extends
Fluxome
> - Class in
sbrt.kernel.fba.proc
This class is used to analyze the activity of fluxes.
FluxActivityProcess(F)
- Constructor for class sbrt.kernel.fba.proc.
FluxActivityProcess
Constructs a new flux activity process.
FluxActivityProcess.Results
- Class in
sbrt.kernel.fba.proc
This class is used to represent the results of a flux activity process.
FluxCapComputer
- Class in
sbrt.kernel.fba.comp
This class is used to compute
flux caps
for use in Mahadevan-Schilling flux interval computations.
FluxCapComputer(IrrevRxnFluxome, DoubleMatrix<?, String>)
- Constructor for class sbrt.kernel.fba.comp.
FluxCapComputer
Constructs a new flux cap computer from the cycles contained in the provided fluxome.
FluxCapComputer(IrrevRxnFluxome, Collection<LinearComb<String>>)
- Constructor for class sbrt.kernel.fba.comp.
FluxCapComputer
Constructs a new flux cap computer from the cycles contained in the provided fluxome.
FluxCapException
- Exception in
sbrt.kernel.fba.comp
This class is used to indicate that a flux cap is invalid.
FluxCapException(MathExpr<String>, String, Throwable)
- Constructor for exception sbrt.kernel.fba.comp.
FluxCapException
Constructs a new flux cap exception.
FluxCapException(MathExpr<String>, String)
- Constructor for exception sbrt.kernel.fba.comp.
FluxCapException
Constructs a new flux cap exception.
FluxCapFormat
- Interface in
sbrt.shell.text.fba
This interface is used to represent the formats of lines of flux cap-containing files.
FluxCapFormatV1
- Class in
sbrt.shell.text.fba
This class is a concrete implementation of
FluxCapFormat
.
FluxCapFormatV1(Fluxome)
- Constructor for class sbrt.shell.text.fba.
FluxCapFormatV1
Constructs a new flux cap file line format using the provided fluxome.
FluxCapInputFile
- Class in
sbrt.shell.io.fba
This class is used to read files containing flux caps.
FluxCapInputFile(String, FluxCapFormat)
- Constructor for class sbrt.shell.io.fba.
FluxCapInputFile
Constructs a new flux cap input file.
FluxCapManager
- Class in
sbrt.shell.mng.fba
This class is used to manage flux cap processes.
FluxCapManager()
- Constructor for class sbrt.shell.mng.fba.
FluxCapManager
FluxCapProcess
- Class in
sbrt.kernel.fba.proc
This class is used to perform a flux cap identification.
FluxCapProcess(FluxCapComputer)
- Constructor for class sbrt.kernel.fba.proc.
FluxCapProcess
Constructs a new flux cap process.
FluxConstraints
- Class in
sbrt.kernel.fba
This class is used to group sets of flux constraints.
FluxConstraints(Map<String, Interval>, Map<? extends MathExpr<String>, Interval>)
- Constructor for class sbrt.kernel.fba.
FluxConstraints
Constructs a set of FBA constraints from the provided arguments.
FluxConstraints(Map<String, Interval>)
- Constructor for class sbrt.kernel.fba.
FluxConstraints
Constructs a set of FBA constraints from the provided argument.
FluxCvComputer
<
F
extends
Fluxome
> - Interface in
sbrt.kernel.fba.comp
This interface is used to represent a flux constraint variation computer.
FluxIntervalAnalyzer
- Class in
sbrt.kernel.fba.analysis
This class is used to analyze flux intervals.
FluxIntervalAnalyzer()
- Constructor for class sbrt.kernel.fba.analysis.
FluxIntervalAnalyzer
FluxIntervalComputer
<
F
extends
Fluxome
> - Interface in
sbrt.kernel.fba.comp
This interface is used to represent flux interval computers.
FluxIntervalInputFile
- Class in
sbrt.shell.io.fba
This class is used to read flux interval input files.
FluxIntervalInputFile(String, FileFormat, Set<LinearComb<String>>, MapFormat<LinearComb<String>, Interval>, Fluxome, double)
- Constructor for class sbrt.shell.io.fba.
FluxIntervalInputFile
Constructs a new flux-interval input file.
FluxIntervalProcess
<
F
extends
Fluxome
> - Class in
sbrt.kernel.fba.proc
This class is used to perform flux interval computations.
FluxIntervalProcess(FluxIntervalComputer<F>)
- Constructor for class sbrt.kernel.fba.proc.
FluxIntervalProcess
Constructs a new flux interval process.
Fluxome
- Interface in
sbrt.kernel.fba
This interface is used to represent fluxomes for use in Flux Balance Analysis.
FluxomeReducer
<
T
extends
Fluxome
> - Interface in
sbrt.kernel.fba.comp
This interface is used to represent algorithms that reduce the size of fluxomes.
FluxomeReducerProcess
<
T
extends
Fluxome
> - Class in
sbrt.kernel.fba.proc
This class is used to execute fluxome reduction processes.
FluxomeReducerProcess(T, FluxomeReducer<T>)
- Constructor for class sbrt.kernel.fba.proc.
FluxomeReducerProcess
Constructs a new fluxome reduction process.
FluxomeSolFileLineFormatV1
- Class in
sbrt.shell.text.fba
This class is a concrete implemenation of
FluxomeSolutionFileLineFormat
.
FluxomeSolFileLineFormatV1(Fluxome)
- Constructor for class sbrt.shell.text.fba.
FluxomeSolFileLineFormatV1
Constructs a new fluxome solution file line format.
FluxomeSolFileLineFormatV1(Fluxome, double)
- Constructor for class sbrt.shell.text.fba.
FluxomeSolFileLineFormatV1
Constructs a new fluxome solution file line format.
FluxomeSolutionFileLineFormat
- Interface in
sbrt.shell.text.fba
This interface is used to represent formats for solutions to the linear system of equations formed by a fluxome.
FluxPlasticityManager
- Class in
sbrt.shell.mng.fba
This class is used to manage flux plasticity processes.
FluxPlasticityManager()
- Constructor for class sbrt.shell.mng.fba.
FluxPlasticityManager
FluxPlasticityProcess
<
F
extends
Fluxome
> - Class in
sbrt.kernel.fba.proc
This class is used to analyze the plasticity of fluxes.
FluxPlasticityProcess(F)
- Constructor for class sbrt.kernel.fba.proc.
FluxPlasticityProcess
Constructs a new flux plasticity process.
FluxPlasticityProcess.Results
- Class in
sbrt.kernel.fba.proc
This class is used to represent the results of a flux plasticity process.
FluxRangeException
- Exception in
sbrt.kernel.fba.comp
This class is used to indicate that the range of a flux interval has exceeded a defined cutoff value.
FluxRangeException(double, Object, String)
- Constructor for exception sbrt.kernel.fba.comp.
FluxRangeException
Constructs a new flux range exception.
FluxRangeException(double, Object)
- Constructor for exception sbrt.kernel.fba.comp.
FluxRangeException
Constructs a new flux range exception.
FluxVectorFormat
- Interface in
sbrt.shell.text.fba
This interface is used to represent formats for flux vectors.
FluxVectorFormatV1
- Class in
sbrt.shell.text.fba
This class is a concrete implemenation of
FluxVectorFormat
.
FluxVectorFormatV1(Fluxome)
- Constructor for class sbrt.shell.text.fba.
FluxVectorFormatV1
Constructs a new flux vector format.
format(Set<? extends E>)
- Method in class sbrt.shell.text.
AbstractLinkedHashSetFormat
Returns a formatted string representation of the provided collection.
format(List<? extends E>)
- Method in class sbrt.shell.text.
AbstractListFormat
Returns a formatted string representation of the provided collection.
format(Boolean)
- Method in interface sbrt.shell.text.
BooleanFormat
Returns a formatted string representation of the provided boolean value.
format(boolean)
- Method in interface sbrt.shell.text.
BooleanFormat
Returns a formatted string representation of the provided boolean value.
format(Or<And<E>>)
- Method in class sbrt.shell.text.
BoolRelFormatV1
Returns a formatted string representation of the provided boolean relationship.
format(String)
- Method in class sbrt.shell.text.chem.
CatalystFormatV1
Returns the provided catalyst name after ensuring it conforms to this format.
format(String)
- Method in class sbrt.shell.text.chem.
CatalystFormatV2
Returns the provided catalyst name after ensuring it conforms to this format.
format(String)
- Method in class sbrt.shell.text.chem.
ChemSpeciesFormatV1
Returns the provided chemical species name after ensuring it conforms to this format.
format(IrrevRxn)
- Method in class sbrt.shell.text.chem.
IrrevRxnFormatV1
Returns a formatted string representation of the provided irreversible chemical reaction.
format(RevRxn)
- Method in class sbrt.shell.text.chem.
RevRxnFormatV1
Returns a formatted string representation of the provided reversible chemical reaction.
format(String)
- Method in class sbrt.shell.text.chem.
RxnNameFormatV1
Returns the provided reaction name after ensuring it conforms to this format.
format(Collection<? extends E>)
- Method in interface sbrt.shell.text.
CollectionFormat
Returns a formatted string representation of the provided collection.
format(Double)
- Method in interface sbrt.shell.text.
DoubleFormat
Returns a formatted string representation of the provided double precision number.
format(double)
- Method in interface sbrt.shell.text.
DoubleFormat
Returns a formatted string representation of the provided double precision number.
format(Double)
- Method in class sbrt.shell.text.
DoubleFormatV1
Returns a formatted string representation of the provided double precision number.
format(double)
- Method in class sbrt.shell.text.
DoubleFormatV1
Parses the provided string and returns its corresponding double precision number.
format(Double)
- Method in class sbrt.shell.text.
DoubleFormatV2
Returns a formatted string representation of the provided double precision number.
format(double)
- Method in class sbrt.shell.text.
DoubleFormatV2
Parses the provided string and returns its corresponding double precision number.
format(List<String>)
- Method in interface sbrt.shell.text.fba.
CatalystListFormat
Returns a formatted string representation of the provided list of catalyst names.
format(List<String>)
- Method in class sbrt.shell.text.fba.
CatalystListFormatV1
Returns a formatted string representation of the provided list of catalyst names.
format(Set<String>)
- Method in interface sbrt.shell.text.fba.
CatalystSetFormat
Returns a formatted string representation of the provided set of enzyme names.
format(Set<String>)
- Method in class sbrt.shell.text.fba.
CatalystSetFormatV1
Returns a formatted string representation of the provided set of catalyst names.
format(String)
- Method in class sbrt.shell.text.fba.
CatalystVerifier
Returns the provided catalyst name after ensuring it exists in the corresponding fluxome of this catalyst name verifier.
format(String)
- Method in class sbrt.shell.text.fba.
ChemSpeciesVerifier
Returns the provided chemical species after ensuring it exists in the corresponding fluxome of this chemical species verifier.
format(String)
- Method in class sbrt.shell.text.fba.
FbaOptHeaderFormatterV1
Returns a formatted string representation of the provided header.
format(ChemRxn)
- Method in class sbrt.shell.text.fba.
IrrevRxnFormatV1
Returns a formatted string representation of the provided irreversible chemical reaction.
format(IrrevRxn)
- Method in class sbrt.shell.text.fba.
IrrevRxnFormatV1
Returns a formatted string representation of the provided irreversible chemical reaction.
format(SourceRxn)
- Method in class sbrt.shell.text.fba.
IrrevRxnFormatV1
Returns a formatted string representation of the provided source.
format(SinkRxn)
- Method in class sbrt.shell.text.fba.
IrrevRxnFormatV1
Returns a formatted string representation of the provided sink.
format(ChemRxn)
- Method in class sbrt.shell.text.fba.
IrrevRxnFormatV2
Returns a formatted string representation of the provided irreversible chemical reaction.
format(IrrevRxn)
- Method in class sbrt.shell.text.fba.
IrrevRxnFormatV2
Returns a formatted string representation of the provided irreversible chemical reaction.
format(SourceRxn)
- Method in class sbrt.shell.text.fba.
IrrevRxnFormatV2
Returns a formatted string representation of the provided source.
format(SinkRxn)
- Method in class sbrt.shell.text.fba.
IrrevRxnFormatV2
Returns a formatted string representation of the provided sink.
format(ChemRxn)
- Method in class sbrt.shell.text.fba.
RevRxnFormatV1
Returns a formatted string representation of the provided irreversible chemical reaction.
format(RevRxn)
- Method in class sbrt.shell.text.fba.
RevRxnFormatV1
Returns a formatted string representation of the provided irreversible chemical reaction.
format(RevExchRxn)
- Method in class sbrt.shell.text.fba.
RevRxnFormatV1
Returns a formatted string representation of the provided source.
format(ChemRxn)
- Method in class sbrt.shell.text.fba.
RevRxnFormatV2
Returns a formatted string representation of the provided irreversible chemical reaction.
format(RevRxn)
- Method in class sbrt.shell.text.fba.
RevRxnFormatV2
Returns a formatted string representation of the provided irreversible chemical reaction.
format(RevExchRxn)
- Method in class sbrt.shell.text.fba.
RevRxnFormatV2
Returns a formatted string representation of the provided source.
format(ChemRxn)
- Method in class sbrt.shell.text.fba.
RxnFormatV1
Returns a formatted string representation of the provided irreversible chemical reaction.
format(IrrevRxn)
- Method in class sbrt.shell.text.fba.
RxnFormatV1
Returns a formatted string representation of the provided irreversible reaction.
format(SourceRxn)
- Method in class sbrt.shell.text.fba.
RxnFormatV1
Returns a formatted string representation of the provided source reaction.
format(SinkRxn)
- Method in class sbrt.shell.text.fba.
RxnFormatV1
Returns a formatted string representation of the provided sink reaction.
format(RevRxn)
- Method in class sbrt.shell.text.fba.
RxnFormatV1
Returns a formatted string representation of the provided reversible reaction.
format(RevExchRxn)
- Method in class sbrt.shell.text.fba.
RxnFormatV1
Returns a formatted string representation of the provided reversible exchange reaction.
format(LinearComb<String>)
- Method in class sbrt.shell.text.fba.
RxnNameExprFormatV1
Returns a formatted string representation of the provided linear combination of reaction names.
format(List<String>)
- Method in interface sbrt.shell.text.fba.
RxnNameListFormat
Returns a formatted string representation of the provided list of reaction names.
format(List<String>)
- Method in class sbrt.shell.text.fba.
RxnNameListFormatV1
Returns a formatted string representation of the provided list of reaction names.
format(Object)
- Method in class sbrt.shell.text.fba.
RxnNameOrExprFormatV1
Returns the string representation of the provided object.
format(Set<String>)
- Method in interface sbrt.shell.text.fba.
RxnNameSetFormat
Returns a formatted string representation of the provided set of reaction names.
format(Set<String>)
- Method in class sbrt.shell.text.fba.
RxnNameSetFormatV1
Returns a formatted string representation of the provided set of reaction names.
format(String)
- Method in class sbrt.shell.text.fba.
RxnNameVerifier
Returns the provided reaction name after ensuring it exists in the corresponding fluxome of this reaction name checker.
format(FileFormat)
- Method in class sbrt.shell.text.
FileFormatFormat
Returns a formatted string representation of the provided file format.
Format
- Interface in
sbrt.shell.text
This interface is used to represent formats.
format(S)
- Method in interface sbrt.shell.text.
Formatter
Returns a formatted string representation of the provided object.
format(Integer)
- Method in interface sbrt.shell.text.
IntegerFormat
Returns a formatted string representation of the provided integer.
format(int)
- Method in interface sbrt.shell.text.
IntegerFormat
Returns a formatted string representation of the provided integer.
format(Integer)
- Method in class sbrt.shell.text.
IntegerFormatV1
Returns a formatted string representation of the provided integer.
format(int)
- Method in class sbrt.shell.text.
IntegerFormatV1
Parses the provided string and returns its corresponding integer.
format(Set<? extends E>)
- Method in interface sbrt.shell.text.
LinkedHashSetFormat
Returns a formatted string representation of the provided set.
format(List<? extends E>)
- Method in interface sbrt.shell.text.
ListFormat
Returns a formatted string representation of the provided list.
format(Long)
- Method in interface sbrt.shell.text.
LongFormat
Returns a formatted string representation of the provided long.
format(long)
- Method in interface sbrt.shell.text.
LongFormat
Returns a formatted string representation of the provided long.
format(Long)
- Method in class sbrt.shell.text.
LongFormatV1
Returns a formatted string representation of the provided long.
format(long)
- Method in class sbrt.shell.text.
LongFormatV1
Parses the provided string and returns its corresponding long.
format(Interval)
- Method in class sbrt.shell.text.math.
BoundedIntervalFormatV1
Returns a formatted string representation of the provided interval.
format(Double)
- Method in interface sbrt.shell.text.math.
CoeffFormat
Returns a formatted string representation of the provided coefficient.
format(double)
- Method in interface sbrt.shell.text.math.
CoeffFormat
Returns a formatted string representation of the provided coefficient.
format(Double)
- Method in class sbrt.shell.text.math.
CoeffFormatV1
Returns a formatted string representation of the provided coefficient.
format(double)
- Method in class sbrt.shell.text.math.
CoeffFormatV1
Returns a formatted string representation of the provided coefficient.
format(Double)
- Method in class sbrt.shell.text.math.
CoeffFormatV2
Returns a formatted string representation of the provided coefficient.
format(double)
- Method in class sbrt.shell.text.math.
CoeffFormatV2
Returns a formatted string representation of the provided coefficient.
format(TauResult)
- Method in class sbrt.shell.text.math.
CorrResFormatterV1
Returns a formatted string representation of the provided correlation results.
format(DirectedGraph.Edge<N>)
- Method in class sbrt.shell.text.math.
DirEdgeFormatV1
Returns a formatted string representation of the provided edge.
format(IndexPair<R, C>)
- Method in class sbrt.shell.text.math.
IndexPairFormatV1
Returns a formatted string representation of the provided index pair.
format(Interval)
- Method in class sbrt.shell.text.math.
IntervalFormatV1
Returns a formatted string representation of the provided interval.
format(LinearComb.Term<? extends V>)
- Method in class sbrt.shell.text.math.
LinCombTermFormatV1
Returns a formatted string representation of the provided term.
format(LinearComb.Term<? extends V>)
- Method in class sbrt.shell.text.math.
LinCombTermFormatV2
Returns a formatted string representation of the provided term.
format(LinearComb<V>)
- Method in interface sbrt.shell.text.math.
LinearCombFormat
Returns a formatted string representation of the provided linear combination.
format(LinearComb<V>)
- Method in class sbrt.shell.text.math.
LinearCombFormatV1
Returns a formatted string representation of the provided linear combination.
format(LinearComb<V>)
- Method in class sbrt.shell.text.math.
LinearCombFormatV2
Returns a formatted string representation of the provided linear combination.
format(LinearComb.Term<? extends V>)
- Method in interface sbrt.shell.text.math.
LinearCombTermFormat
Returns a formatted string representation of the provided term.
format(E)
- Method in interface sbrt.shell.text.math.
MathExprFormat
Returns a formatted string representation of the provided linear combination.
format(MatrixElement<R, C, Double>)
- Method in class sbrt.shell.text.math.
MatrixElementFormatV1
Returns a formatted string representation of the provided matrix element.
format(OptSense)
- Method in class sbrt.shell.text.math.
SenseFormat
Returns a formatted string representation of the provided optimization sense.
format(String)
- Method in class sbrt.shell.text.
NonEmptyStringFormat
Returns the provided string.
format(Double)
- Method in interface sbrt.shell.text.
PercentFormat
Returns a formatted string representation of the provided percentage.
format(double)
- Method in interface sbrt.shell.text.
PercentFormat
Returns a formatted string representation of the provided percentage.
format(double)
- Method in class sbrt.shell.text.
PercentFormatVersion1
Returns a formatted string representation of the provided percentage.
format(Double)
- Method in class sbrt.shell.text.
PercentFormatVersion1
Returns a formatted string representation of the provided percentage.
format(List<E>)
- Method in class sbrt.shell.text.
SimpleListFormat
Returns a formatted string representation of the provided list.
format(Set<E>)
- Method in class sbrt.shell.text.
SimpleSetFormat
Returns a formatted string representation of the provided set.
format(String)
- Method in class sbrt.shell.text.
StringFormat
Returns the provided string.
format(Boolean)
- Method in class sbrt.shell.text.
TrueFalseFormat
Returns "true" or "false" depending on the provided boolean value.
format(boolean)
- Method in class sbrt.shell.text.
TrueFalseFormat
Returns "true" or "false" depending on the provided boolean value.
format(Boolean)
- Method in class sbrt.shell.text.
YesNoFormat
Returns "Yes" or "No" depending on the provided boolean value.
format(boolean)
- Method in class sbrt.shell.text.
YesNoFormat
Returns "Yes" or "No" depending on the provided boolean value.
formatElement(MatrixElement<? extends R, ? extends C, Double>)
- Method in class sbrt.shell.text.math.
MatrixElementFormatV1
Returns a formatted string representation of the provided matrix element.
FormatException
- Exception in
sbrt.shell.text
This exception type is used to indicate a formatting error has ocurred.
FormatException(String)
- Constructor for exception sbrt.shell.text.
FormatException
Constructs a new format exception with the provided error message.
FormatException(String, Throwable)
- Constructor for exception sbrt.shell.text.
FormatException
Constructs a new format exception with the provided error message and cause.
formatKey(S)
- Method in class sbrt.shell.text.
AbstractMapFormat
Returns a formatted string representation of the provided key.
formatKey(S)
- Method in class sbrt.shell.text.
ColonMapEntryFormatV1
Returns a formatted string representation of the provided key object.
formatKey(S)
- Method in class sbrt.shell.text.
EqualsMapEntryFormatV1
Returns a formatted string representation of the provided key object.
formatKey(String)
- Method in class sbrt.shell.text.fba.
FbaOptFileLineFormatV1
Returns a formatted string representation of the provided key.
formatKey(S)
- Method in interface sbrt.shell.text.
MapEntryFormat
Returns a formatted string representation of the provided key.
formatKey(T)
- Method in interface sbrt.shell.text.
MapFormat
Returns a formatted string representation of the provided key.
formatKeys(Set<? extends K>)
- Method in class sbrt.shell.text.
AbstractMapFormat
Returns a formatted string representation of the provided set of keys.
formatKeys(Set<? extends String>)
- Method in class sbrt.shell.text.fba.
FbaOptFileLineFormatV1
Returns a formatted string representation of the provided set of keys.
formatKeys(Set<? extends K>)
- Method in interface sbrt.shell.text.
MapFormat
Returns a formatted string representation of the provided set of keys.
formatPair(S, T)
- Method in class sbrt.shell.text.
AbstractMapEntryFormat
Returns a string representation of the provided key-value pair.
formatPair(Map.Entry<? extends K, ? extends V>)
- Method in class sbrt.shell.text.
AbstractMapEntryFormat
Returns a formatted string representation of the provided map entry.
formatPair(S, T)
- Method in class sbrt.shell.text.
AbstractMapFormat
Returns a string representation of the provided key-value pair.
formatPair(Map.Entry<? extends K, ? extends V>)
- Method in class sbrt.shell.text.
AbstractMapFormat
Returns a formatted string representation of the provided map entry.
formatPair(String, Double)
- Method in class sbrt.shell.text.fba.
FbaOptFileLineFormatV1
Returns a string representation of the provided key-value pair.
formatPair(Map.Entry<? extends String, ? extends Double>)
- Method in class sbrt.shell.text.fba.
FbaOptFileLineFormatV1
Returns a formatted string representation of the provided map entry.
formatPair(S, T)
- Method in interface sbrt.shell.text.
MapEntryFormat
Returns a formatted string representation of the provided key-value pair.
formatPair(Map.Entry<? extends K, ? extends V>)
- Method in interface sbrt.shell.text.
MapEntryFormat
Returns a formatted string representation of the provided key-value pair.
formatPair(S, T)
- Method in interface sbrt.shell.text.
MapFormat
Returns a formatted string representation of the provided key-value pair.
formatPair(Map.Entry<? extends K, ? extends V>)
- Method in interface sbrt.shell.text.
MapFormat
Returns a formatted string representation of the provided key-value pair.
formatPair(IndexPair<? extends R, ? extends C>)
- Method in class sbrt.shell.text.math.
IndexPairFormatV1
Returns a formatted string representation of the provided index pair.
Formatter
<
T
> - Interface in
sbrt.shell.text
This interface is used to represent
formatters
.
formatValue(T)
- Method in class sbrt.shell.text.
AbstractMapFormat
Returns a formatted string representation of the provided value.
formatValue(T)
- Method in class sbrt.shell.text.
ColonMapEntryFormatV1
Returns a formatted string representation of the provided value object.
formatValue(T)
- Method in class sbrt.shell.text.
EqualsMapEntryFormatV1
Returns a formatted string representation of the provided value object.
formatValue(Double)
- Method in class sbrt.shell.text.fba.
FbaOptFileLineFormatV1
Returns a formatted string representation of the provided value.
formatValue(T)
- Method in interface sbrt.shell.text.
MapEntryFormat
Returns a formatted string representation of the provided value.
formatValue(T)
- Method in interface sbrt.shell.text.
MapFormat
Returns a formatted string representation of the provided value.
formatValues(List<? extends V>)
- Method in class sbrt.shell.text.
AbstractMapFormat
Returns a string representation of the provided list of values.
formatValues(Map<? extends K, ? extends V>)
- Method in class sbrt.shell.text.
AbstractMapFormat
Returns a string representation of the values in the provided map formatted as a list.
formatValues(List<? extends Double>)
- Method in class sbrt.shell.text.fba.
FbaOptFileLineFormatV1
Returns a string representation of the provided list of values.
formatValues(Map<? extends String, ? extends Double>)
- Method in class sbrt.shell.text.fba.
FbaOptFileLineFormatV1
Returns a string representation of the values in the provided map formatted as a list.
formatValues(List<? extends V>)
- Method in interface sbrt.shell.text.
MapFormat
Returns a string representation of the provided list of values.
formatValues(Map<? extends K, ? extends V>)
- Method in interface sbrt.shell.text.
MapFormat
Returns a string representation of the values in the provided map formatted as a list.
FORWARD_SLASH
- Static variable in class sbrt.shell.text.
SpecialChars
/
FORWARD_SUFFIX
- Static variable in class sbrt.kernel.fba.proc.
RevRxnBreakerProcess
The default suffix added to the names or IDs of forward reactions.
freeVariables()
- Method in class sbrt.kernel.math.algebra.
HashLinearSystemSolution
Returns the number of free variables in this solution.
freeVariables()
- Method in interface sbrt.kernel.math.algebra.
LinearSystemSolution
Returns the number of free variables in this solution.
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