A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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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