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

S

S_MATRIX_FILE_NAME - Static variable in class sbrt.shell.mng.fba.NetworkInfoManager
The keyword used to denote the name of the file to which the stoichiometry matrix of a fluxome will be written.
SAFETY_LEVEL - Static variable in class sbrt.shell.mng.fba.FbaOptManager
The keyword used to denote the safety level.
SAMPLE_A_FILE - Static variable in class sbrt.shell.mng.stat.MannWhitneyUManager
The keyword used to denote the name of the file containing sample A.
SAMPLE_B_FILE - Static variable in class sbrt.shell.mng.stat.MannWhitneyUManager
The keyword used to denote the name of the file containing sample B.
SBML_INPUT_FILE - Static variable in class sbrt.shell.mng.fba.BiggSbmlReaderManager
The keyword used to denote the name of the SBML input file.
SBML_INPUT_FILE - Static variable in class sbrt.shell.mng.fba.PalssonSbmlReaderManager
The keyword used to denote the name of the SBML input file.
sbrt - package sbrt
Provides the class used to run the Systems Biology Research Tool.
Sbrt - Class in sbrt
This class is used to execute the Systems Biology Research Tool as an application.
Sbrt() - Constructor for class sbrt.Sbrt
 
sbrt.ext - package sbrt.ext
Provides classes that allow the Systems Biology Research Tool to encapsulate external software.
sbrt.ext.cplex - package sbrt.ext.cplex
Provides a class that allows communication with CPLEX.
sbrt.ext.glpk - package sbrt.ext.glpk
Provides a class that allows communication with GLPK.
sbrt.ext.mma - package sbrt.ext.mma
Provides classes that allow communication with Mathematica.
sbrt.ext.mma.algebra - package sbrt.ext.mma.algebra
Provides classes that allow communication with Mathematica for the purposes of algebra.
sbrt.ext.R - package sbrt.ext.R
Provides classes that allow communication with R.
sbrt.ext.R.stat - package sbrt.ext.R.stat
Provides classes that allow communication with R for the purposes of statistics.
sbrt.kernel - package sbrt.kernel
Provides interfaces to define processes.
sbrt.kernel.fba - package sbrt.kernel.fba
Provides classes and interfaces for creating objects relevant to Flux Balance Analysis.
sbrt.kernel.fba.analysis - package sbrt.kernel.fba.analysis
Provides classes and interfaces for analyzing Flux Balance Analysis data.
sbrt.kernel.fba.comp - package sbrt.kernel.fba.comp
Provides classes and interfaces for performing Flux Balance Analysis computations.
sbrt.kernel.fba.proc - package sbrt.kernel.fba.proc
Provides classes and interfaces for executing Flux Balance Analysis processes.
sbrt.kernel.io - package sbrt.kernel.io
Provides classes and interfaces used to perform kernel-level I/O.
sbrt.kernel.math - package sbrt.kernel.math
Provides classes and interfaces for creating objects relevant to mathematics.
sbrt.kernel.math.algebra - package sbrt.kernel.math.algebra
Provides classes and interfaces for creating objects relevant to algebra.
sbrt.kernel.math.algebra.proc - package sbrt.kernel.math.algebra.proc
Provides classes and interfaces for executing algebra-related processes.
sbrt.kernel.math.comb.comp - package sbrt.kernel.math.comb.comp
Provides classes and interfaces for performing combinatorial analysis-related computations.
sbrt.kernel.math.comb.proc - package sbrt.kernel.math.comb.proc
Provides classes and interfaces for performing combinatorial analysis-related processes.
sbrt.kernel.math.geom - package sbrt.kernel.math.geom
Provides classes and interfaces for creating objects relevant to computational geometry.
sbrt.kernel.math.geom.comp - package sbrt.kernel.math.geom.comp
Provides classes and interfaces for performing geometry-related computations.
sbrt.kernel.math.geom.proc - package sbrt.kernel.math.geom.proc
Provides classes and interfaces for performing geometry-related processes.
sbrt.kernel.math.graph_theory - package sbrt.kernel.math.graph_theory
Provides classes and interfaces for creating objects relevant to graph theory.
sbrt.kernel.math.graph_theory.comp - package sbrt.kernel.math.graph_theory.comp
Provides classes and interfaces for performing graph theoretical computations.
sbrt.kernel.math.graph_theory.proc - package sbrt.kernel.math.graph_theory.proc
Provides classes and interfaces for performing graph theoretical processes.
sbrt.kernel.math.optimization - package sbrt.kernel.math.optimization
Provides classes and interfaces for creating objects relevant to solving optimization problems.
sbrt.kernel.math.stat - package sbrt.kernel.math.stat
Provides classes and interfaces for creating objects relevant to statistics.
sbrt.kernel.math.stat.comp - package sbrt.kernel.math.stat.comp
Provides classes and interfaces for performing statistical computations.
sbrt.kernel.math.stat.proc - package sbrt.kernel.math.stat.proc
Provides classes and interfaces for performing statistical processes.
sbrt.kernel.utilities - package sbrt.kernel.utilities
Provides classes and interfaces for performing utility functions.
sbrt.kernel.utilities.proc - package sbrt.kernel.utilities.proc
Provides classes and interfaces for performing utility processes.
sbrt.shell - package sbrt.shell
Provides classes used by shell-level software.
sbrt.shell.gui - package sbrt.shell.gui
Provides classes for creating graphical user interfaces for the SBRT.
sbrt.shell.io - package sbrt.shell.io
Provides classes and interfaces for reading and writing files.
sbrt.shell.io.fba - package sbrt.shell.io.fba
Provides classes and interfaces for reading and writing files relevant to Flux Balance Analysis.
sbrt.shell.mng - package sbrt.shell.mng
Provides classes and interfaces for creating process managers.
sbrt.shell.mng.algebra - package sbrt.shell.mng.algebra
Provides classes for creating algebra process managers.
sbrt.shell.mng.comb - package sbrt.shell.mng.comb
Provides classes for creating combinatorics process managers.
sbrt.shell.mng.fba - package sbrt.shell.mng.fba
Provides classes and interfaces for creating Flux Balance Analysis process managers.
sbrt.shell.mng.geom - package sbrt.shell.mng.geom
Provides classes and for creating geometry process managers.
sbrt.shell.mng.graph_theory - package sbrt.shell.mng.graph_theory
Provides classes and for creating graph theoretical process managers.
sbrt.shell.mng.stat - package sbrt.shell.mng.stat
Provides classes and interfaces for creating statistical process managers.
sbrt.shell.mng.utilities - package sbrt.shell.mng.utilities
Provides classes and interfaces for creating mathematical process managers.
sbrt.shell.proc.fba - package sbrt.shell.proc.fba
Provides classes for converting FBA-related files of different formats.
sbrt.shell.text - package sbrt.shell.text
Provides classes and interfaces for defining formats for basic objects.
sbrt.shell.text.chem - package sbrt.shell.text.chem
Provides classes and interfaces for defining formats for chemistry related objects.
sbrt.shell.text.fba - package sbrt.shell.text.fba
Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis.
sbrt.shell.text.math - package sbrt.shell.text.math
Provides classes and interfaces for defining formats for mathematical objects.
SbrtFile - Interface in sbrt.shell.io
This interface is used to represent files.
SbrtOutputPane - Class in sbrt.shell.gui
This class is used to create the output pane of the SBRT GUI where text is written by each process.
SbrtOutputPane() - Constructor for class sbrt.shell.gui.SbrtOutputPane
Creates a new SBRT GUI output pane.
SEED - Static variable in class sbrt.shell.mng.AbstractProcessManager
The keword used to denote the seed to a pseudorandom number generator.
SEMICOLON - Static variable in class sbrt.shell.text.SpecialChars
;
SenseFormat - Class in sbrt.shell.text.math
This class is used to represent formats of optimization senses.
SenseFormat() - Constructor for class sbrt.shell.text.math.SenseFormat
 
SerFbaOptOutputFile<F extends Fluxome> - Class in sbrt.shell.io.fba
This class is used to write output files containing FBA optimization data as serialized maps.
SerFbaOptOutputFile(String, FileFormat, Set<String>, FbaOptFileLineFormat) - Constructor for class sbrt.shell.io.fba.SerFbaOptOutputFile
Constructs a new serialized FBA optimization output file.
SERIALIZED - Static variable in class sbrt.shell.io.FileFormat
Used to denote a file containing serialized objects.
SerializedFileIterator<E> - Class in sbrt.shell.io
This class is used to iterate over the objects in a serialized input file.
SerializedFileIterator(SerializedInputFile<E>) - Constructor for class sbrt.shell.io.SerializedFileIterator
Constructs a new serialized file iterator using the provided serialized input file.
SerializedInputFile<E> - Class in sbrt.shell.io
This class is used to read input files containing serialized objects.
SerializedInputFile(String) - Constructor for class sbrt.shell.io.SerializedInputFile
Constructs a new text input file using the provided argument.
SerializedInputFile(String, FileFormat) - Constructor for class sbrt.shell.io.SerializedInputFile
Constructs a new text input file using the provided arguments.
SerializedMapInputFile<K,V> - Class in sbrt.shell.io
This class is used to read input files containing serialized maps.
SerializedMapInputFile(String, FileFormat) - Constructor for class sbrt.shell.io.SerializedMapInputFile
Constructs a new input file using the provided arguments.
SerializedMapInputFile(String, FileFormat, Set<? extends K>) - Constructor for class sbrt.shell.io.SerializedMapInputFile
Constructs a new input file using the provided arguments.
SerializedOutputFile<E> - Class in sbrt.shell.io
This class is used to write serialized objects to output files.
SerializedOutputFile(String, FileFormat) - Constructor for class sbrt.shell.io.SerializedOutputFile
Constructs a new serialized output file from the provided arguments.
set(int, E) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.set(int, Object).
set(File) - Static method in class sbrt.shell.WorkingDirectory
Sets the working directory to the provided value.
set(String) - Static method in class sbrt.shell.WorkingDirectory
Sets the working directory to the provided value.
setActiveFluxes(int) - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Sets the total number of active fluxes to be contained in each randomly generated set of flux constraints.
setCatalystDeletionSource(Iterable<Set<String>>) - Method in class sbrt.kernel.fba.proc.CvCatalystDeletionProcess
Sets the catalyst deletion input source.
setCatalystDelSource(Iterable<Set<String>>) - Method in class sbrt.kernel.fba.proc.CatalystDeletionProcess
Sets the catalyst deletion input source.
setColExprConstraint(MathExpr<?>, Interval) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Changes the constraint on the provided mathematical expression of column variables.
setColExprConstraints(Map<? extends MathExpr<?>, Interval>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Changes the constraints on more than one mathematical expression of column variables.
setColumnConstraint(T, Interval) - Method in class sbrt.ext.cplex.CplexSolver
Sets the constraint on the provided column variable.
setColumnConstraint(Y, Interval) - Method in class sbrt.ext.glpk.GlpkSolver
Sets the constraint on the provided column variable.
setColumnConstraint(Object, Interval) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Changes the constraint of the provided column variable.
setColumnConstraint(Y, Interval) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Sets the constraint on the provided column variable.
setColumnConstraints(Map<? extends C, Interval>) - Method in class sbrt.ext.cplex.CplexSolver
Sets the constraints for the provided column variables.
setColumnConstraints(Map<? extends C, Interval>) - Method in class sbrt.ext.glpk.GlpkSolver
Sets the constraints for the provided column variables.
setColumnConstraints(Map<?, Interval>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Changes the constraints on more than one column variable.
setColumnConstraints(Map<? extends C, Interval>) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Sets the constraints for the provided column variables.
setConstraint(MathExpr<? extends C>, Interval) - Method in class sbrt.ext.cplex.CplexSolver
Sets a constraint on the provided mathematical expression of column variables.
setConstraint(LinearComb<? extends C>, Interval) - Method in class sbrt.ext.cplex.CplexSolver
Sets a constraint on the provided mathematical expression of column variables.
setConstraint(QuadraticExpr<? extends C>, Interval) - Method in class sbrt.ext.cplex.CplexSolver
Sets a constraint on the provided mathematical expression of column variables.
setConstraint(MathExpr<? extends C>, Interval) - Method in class sbrt.ext.glpk.GlpkSolver
Sets a constraint on the provided mathematical expression of column variables.
setConstraint(LinearComb<? extends C>, Interval) - Method in class sbrt.ext.glpk.GlpkSolver
Sets a constraint on the provided mathematical expression of column variables.
setConstraint(LinearComb<? extends C>, Interval) - Method in interface sbrt.kernel.math.optimization.LinearProgramSolver
Sets a constraint on the provided linear combination of column variables.
setConstraint(MathExpr<? extends C>, Interval) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Sets a constraint on the provided mathematical expression of column variables.
setConstraint(QuadraticExpr<? extends C>, Interval) - Method in interface sbrt.kernel.math.optimization.QuadraticProgramSolver
Sets a constraint on the provided quadratic expression of column variables.
setConstraints(Map<? extends MathExpr<? extends C>, Interval>) - Method in class sbrt.ext.cplex.CplexSolver
Sets constraints on the provided mathematical expressions of column variables.
setConstraints(Map<? extends MathExpr<? extends C>, Interval>) - Method in class sbrt.ext.glpk.GlpkSolver
Sets constraints on the provided mathematical expressions of column variables.
setConstraints(FluxConstraints, FluxCvComputer<?>) - Static method in class sbrt.kernel.fba.proc.AbstractCvFbaOptProcess
Sets the provided constraints in the provided constraint-variation computer.
setConstraints(Map<? extends MathExpr<? extends C>, Interval>) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Sets constraints on the provided mathematical expressions of column variables.
setConstraintSource(Iterable<FluxConstraints>) - Method in class sbrt.kernel.fba.proc.CvCatalystDeletionProcess
Sets the constraint variation input source.
setConstraintSource(Iterable<FluxConstraints>) - Method in class sbrt.kernel.fba.proc.CvFbaOptProcess
Sets the constraint variation input source.
setConstraintSource(Iterable<FluxConstraints>) - Method in class sbrt.kernel.fba.proc.CvFluxIntervalProcess
Sets the constraint variation input source.
setConstraintSource(Iterable<FluxConstraints>) - Method in class sbrt.kernel.fba.proc.CvObjectiveFunctionProcess
Sets the constraint variation input source.
setConstraintSource(Iterable<FluxConstraints>) - Method in class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Sets the constraint variation input source.
setConstraintTolerance(double) - Method in class sbrt.kernel.math.geom.comp.CdHarComp
Sets the constraint tolerance.
setConstraintTolerance(double) - Method in class sbrt.kernel.math.geom.proc.CdHarProcess
Sets the constraint tolerance.
setElement(X, Y, double) - Method in class sbrt.kernel.math.algebra.AbstractSmdMatrix
Sets the element at the provided row and column indices to the provided double precision value.
setElement(X, Y, double) - Method in interface sbrt.kernel.math.algebra.DoubleMatrixBuilder
Sets the element at the provided row and column indices to the provided double precision value.
setElement(X, Y, Z) - Method in class sbrt.kernel.math.algebra.HashMatrix
Sets the element at the provided row and column indices to the provided double precision value.
setElement(X, Y, Z) - Method in interface sbrt.kernel.math.algebra.MatrixBuilder
Sets the element at the provided row and column indices to the one provided.
setElement(X, Y, Z) - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Sets the element at the provided row and column indices to the provided double precision value.
setElement(X, Y, Z) - Method in class sbrt.kernel.math.algebra.TreeMatrix
Sets the element at the provided row and column indices to the provided double precision value.
setElements(DoubleMatrix<? extends R, ? extends C>) - Method in class sbrt.kernel.math.algebra.AbstractMdMatrix
Sets the corresponding elements of this matrix to those of the provided matrix.
setElements(Matrix<? extends R, ? extends C, ? extends Double>) - Method in class sbrt.kernel.math.algebra.AbstractSmdMatrix
Sets the corresponding elements of this matrix to those of the provided matrix.
setElements(SparseDoubleMatrix<? extends R, ? extends C>) - Method in class sbrt.kernel.math.algebra.AbstractSmdMatrix
Sets the corresponding elements of this matrix to those of the provided matrix.
setElements(Map<IndexPair<R, C>, Double>) - Method in class sbrt.kernel.math.algebra.AbstractSmdMatrix
Sets the corresponding elements of this matrix to those provided.
setElements(DoubleMatrix<? extends R, ? extends C>) - Method in interface sbrt.kernel.math.algebra.DoubleMatrixBuilder
Sets the corresponding elements of this matrix to those of the provided matrix.
setElements(Matrix<? extends R, ? extends C, ? extends E>) - Method in interface sbrt.kernel.math.algebra.MatrixBuilder
Sets the corresponding elements of this matrix to those of the provided matrix.
setElements(SparseDoubleMatrix<? extends R, ? extends C>) - Method in interface sbrt.kernel.math.algebra.SmdMatrix
Sets the corresponding elements of this matrix to those of the provided matrix.
setEquations(Map<LinearComb<V>, Double>) - Method in class sbrt.kernel.math.algebra.proc.LinearSolverProcess
Sets the system of linear equations to be solver.
setExprs(Collection<? extends E>) - Method in class sbrt.kernel.utilities.proc.VariableParticipation
Sets the collection of mathematical expressions to organize.
setFluxConstraint(String, Interval) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Changes the flux constraint of the reaction with the provided name.
setFluxConstraint(String, Interval) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Changes the flux constraint of the reaction with the provided name.
setFluxConstraint(String, Interval) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Changes the flux constraint of the reaction with the provided name.
setFluxConstraint(String, Interval) - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Changes the flux constraint of the reaction with the provided name.
setFluxConstraint(String, Interval) - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Changes the flux constraint of the reaction with the provided name.
setFluxConstraint(String, Interval) - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Changes the flux constraint of the reaction with the provided name.
setFluxConstraints(Map<String, Interval>) - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Changes the flux constraints on more than one reaction.
setFluxConstraints(Map<String, Interval>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Changes the flux constraints on more than one reaction.
setFluxConstraints(Map<String, Interval>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Changes the flux constraints on more than one reaction.
setFluxConstraints(Map<String, Interval>) - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Changes the flux constraints on more than one reaction.
setFluxConstraints(Map<String, Interval>) - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Changes the flux constraints on more than one reaction.
setFluxIntervalSource(Iterable<Map<String, Interval>>) - Method in class sbrt.kernel.fba.proc.FluxPlasticityProcess
Sets the flux interval source.
setFluxVectorSource(Iterable<Map<String, Double>>) - Method in class sbrt.kernel.fba.proc.FluxActivityProcess
Sets the flux vector source.
setFluxVectorSource(Iterable<Map<String, Double>>) - Method in class sbrt.kernel.fba.proc.SvCdHarFluxVectorProcess
Sets the source of flux vectors to serve as initial points.
setForwardSuffix(String) - Method in class sbrt.kernel.fba.proc.RevRxnBreakerProcess
Sets the forward suffix if a non-default value is desired.
setGraph(DirectedGraph<N>) - Method in class sbrt.kernel.math.graph_theory.proc.CycleIdProcess
Sets the graph for which all cycles will be identified.
setGraph(DirectedGraph<N>) - Method in class sbrt.kernel.math.graph_theory.proc.PathIdProcess
Sets the graph for which all paths will be identified.
setInactive(Interval) - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Sets the constraint used for inactive reactions.
setInitialFluxVector(Map<String, Double>) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Sets the initial flux vector to the one provided.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class plug_in_example.shell.GreetingManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>) - Method in class sbrt.shell.mng.AbstractProcessManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.algebra.LinearCombConverterManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.algebra.LinearSolverManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.algebra.MatrixConverterManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.algebra.MultipleVectorsConverterManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.algebra.SingleVectorConverterManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.comb.SingleElementUnionManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.comb.StrictSingleElementUnionManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.BiggSbmlReaderManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.CatalystDeletionManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.CvCatalystDeletionManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.CvFbaOptManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.CvMsFluxIntervalManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.CvObjectiveFunctionManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.CvRevRxnFluxIntervalManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.CvRxnDeletionManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.CvSimpleFluxIntervalManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.ExtremeCurrentManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.FbaOptManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.FbaSolverManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.FluxActivityManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.FluxCapManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.FluxPlasticityManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.InitialPointManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.MetatoolInputReaderManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.MetatoolInputWriterManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.MetatoolOutputReaderManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.MsFluxIntervalManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.MsFluxomeReducerManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.NetworkInfoManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.ObjectiveFunctionManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.PalssonSbmlReaderManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.RandomConstraintsManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.RandomObjectiveManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.RedundRxnRemoverManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.ReverseRxnFluxIntervalManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.RevRxnBreakerManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.RxnDeletionManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.SimpleRxnFileTransManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.SlpCycleIdManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.fba.WwFluxomeReducerManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.geom.CdHarManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.graph_theory.CycleIdManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.graph_theory.GraphInfoManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.graph_theory.PathIdManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.graph_theory.UniqueCycleIdManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<K, V>) - Method in interface sbrt.shell.mng.ProcessManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<K, V>, PrintWriter) - Method in interface sbrt.shell.mng.ProcessManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.stat.CorrelationManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.stat.KendallTauManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.stat.MannWhitneyUManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.utilities.IntervalComparisonManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.utilities.VariableParticipationManager
Uses the provided input to prepare this process manager for execution.
setInput(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.shell.mng.utilities.VectorComparisonManager
Uses the provided input to prepare this process manager for execution.
setIntervalSource(Iterable<FluxConstraints>) - Method in class sbrt.kernel.fba.proc.SvCdHarFluxVectorProcess
Sets the flux interval input source.
setIntervalSource(Iterable<FluxConstraints>) - Method in class sbrt.kernel.fba.proc.SvInitialPointProcess
Sets the flux interval input source.
setIntervalSources(Iterable<Map<V, Interval>>, Iterable<Map<V, Interval>>) - Method in class sbrt.kernel.utilities.proc.IntervalComparison
Sets of the sources of interval vectors.
setIrrevConstraint(Interval) - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Sets the constraint used for active irreversible reactions.
setIterations(int) - Method in class sbrt.kernel.fba.proc.CdHarFluxVectorProcess
Sets the total number of flux vectors to be generated.
setIterations(int) - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Sets the number of sets of random flux constraints to be produced.
setIterations(int) - Method in class sbrt.kernel.fba.proc.RandomObjectiveGenerator
Sets the number of random objective functions to be produced.
setIterations(int) - Method in class sbrt.kernel.fba.proc.SvCdHarFluxVectorProcess
Sets the total number of flux vectors to be generated.
setIterations(int) - Method in class sbrt.kernel.math.geom.proc.CdHarProcess
Sets the total number of random points to be added to the provided results manager.
setMatrixElement(S, T, double) - Method in class sbrt.ext.cplex.CplexSolver
Sets the element of the program matrix at the provided row and column variables to the one provided.
setMatrixElement(X, Y, double) - Method in class sbrt.ext.glpk.GlpkSolver
Sets the element of the program matrix at the provided row and column variables to the one provided.
setMatrixElement(Object, Object, double) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Sets the specified element of the program matrix to the one provided.
setMatrixElement(X, Y, double) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Sets the element of the program matrix at the provided row and column variables to the one provided.
setMatrixElements(DoubleMatrix<?, ?>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Sets the specified elements of the program matrix to those provided.
setMaxObstructedMoves(int) - Method in class sbrt.kernel.math.geom.proc.CdHarProcess
Sets the maximum number of obstructed moves to allow.
setMaxWastedMoves(int) - Method in class sbrt.kernel.fba.proc.CdHarFluxVectorProcess
Sets the maximum number of wasted moves to allow.
setMinChordLength(double) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Sets the minimum chord length.
setMinChordLength(double) - Method in class sbrt.kernel.math.geom.comp.CdHarComp
Sets the minimum chord length.
setMinChordLength(double) - Method in class sbrt.kernel.math.geom.proc.CdHarProcess
Sets the minimum chord length.
setObjectiveFunction(MathExpr<? extends C>, OptSense) - Method in class sbrt.ext.cplex.CplexSolver
Sets the objective function and optimization sense to the provided values.
setObjectiveFunction(LinearComb<? extends C>, OptSense) - Method in class sbrt.ext.cplex.CplexSolver
Sets the objective function and optimization sense to the provided values.
setObjectiveFunction(QuadraticExpr<? extends C>, OptSense) - Method in class sbrt.ext.cplex.CplexSolver
Sets the objective function and optimization sense to the provided values.
setObjectiveFunction(MathExpr<? extends C>) - Method in class sbrt.ext.cplex.CplexSolver
Sets the objective function to the provided mathematical expression of column variables.
setObjectiveFunction(LinearComb<? extends C>) - Method in class sbrt.ext.cplex.CplexSolver
Sets the objective function to the provided mathematical expression of column variables.
setObjectiveFunction(QuadraticExpr<? extends C>) - Method in class sbrt.ext.cplex.CplexSolver
Not yet implemented.
setObjectiveFunction(MathExpr<? extends C>, OptSense) - Method in class sbrt.ext.glpk.GlpkSolver
Sets the objective function and optimization sense to the provided values.
setObjectiveFunction(MathExpr<? extends C>) - Method in class sbrt.ext.glpk.GlpkSolver
Sets the objective function to the provided mathematical expression of column variables.
setObjectiveFunction(LinearComb<? extends C>, OptSense) - Method in class sbrt.ext.glpk.GlpkSolver
Sets the objective function and optimization sense to the provided values.
setObjectiveFunction(LinearComb<? extends C>) - Method in class sbrt.ext.glpk.GlpkSolver
Sets the objective function to the provided mathematical expression of column variables.
setObjectiveFunction(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Sets the objective function to the provided mathematical expression.
setObjectiveFunction(MathExpr<String>) - Method in class sbrt.kernel.fba.proc.CatalystDeletionProcess
Sets the objective function to the provided mathematical expression.
setObjectiveFunction(MathExpr<String>) - Method in class sbrt.kernel.fba.proc.CvCatalystDeletionProcess
Sets the objective function to the provided mathematical expression.
setObjectiveFunction(MathExpr<String>) - Method in class sbrt.kernel.fba.proc.CvFbaOptProcess
Sets the objective function to the provided mathematical expression.
setObjectiveFunction(MathExpr<String>) - Method in class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Sets the objective function to the provided mathematical expression.
setObjectiveFunction(LinearComb<String>) - Method in class sbrt.kernel.fba.proc.FbaOptProcess
Sets the objective function to the provided mathematical expression.
setObjectiveFunction(MathExpr<String>) - Method in class sbrt.kernel.fba.proc.RxnDeletionProcess
Sets the objective function to the provided mathematical expression.
setObjectiveFunction(LinearComb<? extends C>, OptSense) - Method in interface sbrt.kernel.math.optimization.LinearProgramSolver
Sets the objective function and optimization sense to the provided values.
setObjectiveFunction(LinearComb<? extends C>) - Method in interface sbrt.kernel.math.optimization.LinearProgramSolver
Sets the objective function to the provided linear combination of column variables.
setObjectiveFunction(MathExpr<? extends C>, OptSense) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Sets the objective function and optimization sense to the provided values.
setObjectiveFunction(MathExpr<? extends C>) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Sets the objective function to the provided mathematical expression of column variables.
setObjectiveFunction(QuadraticExpr<? extends C>, OptSense) - Method in interface sbrt.kernel.math.optimization.QuadraticProgramSolver
Sets the objective function and optimization sense to the provided values.
setObjectiveFunction(QuadraticExpr<? extends C>) - Method in interface sbrt.kernel.math.optimization.QuadraticProgramSolver
Sets the objective function to the provided quadratic expression of column variables.
setObjectiveFunctionSource(Iterable<? extends MathExpr<String>>) - Method in class sbrt.kernel.fba.proc.CvObjectiveFunctionProcess
Sets the objective function input source.
setObjectiveFunctionSource(Iterable<? extends MathExpr<String>>) - Method in class sbrt.kernel.fba.proc.ObjFunAnalysis
Sets the objective function input source.
setOptimizationSense(OptSense) - Method in class sbrt.ext.cplex.CplexSolver
Sets the optimization sense.
setOptimizationSense(OptSense) - Method in class sbrt.ext.glpk.GlpkSolver
Sets the optimization sense.
setOptimizationSense(OptSense) - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Sets the optimization sense to the provided value.
setOptimizationSense(OptSense) - Method in class sbrt.kernel.fba.proc.CatalystDeletionProcess
Sets the optimization sense to the provided value.
setOptimizationSense(OptSense) - Method in class sbrt.kernel.fba.proc.CvCatalystDeletionProcess
Sets the optimization sense to the provided value.
setOptimizationSense(OptSense) - Method in class sbrt.kernel.fba.proc.CvFbaOptProcess
Sets the optimization sense to the provided value.
setOptimizationSense(OptSense) - Method in class sbrt.kernel.fba.proc.CvObjectiveFunctionProcess
Sets the optimization sense to the provided value.
setOptimizationSense(OptSense) - Method in class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Sets the optimization sense to the provided value.
setOptimizationSense(OptSense) - Method in class sbrt.kernel.fba.proc.FbaOptProcess
Sets the optimization sense to the provided value.
setOptimizationSense(OptSense) - Method in class sbrt.kernel.fba.proc.ObjFunAnalysis
Sets the optimization sense to the provided value.
setOptimizationSense(OptSense) - Method in class sbrt.kernel.fba.proc.RxnDeletionProcess
Sets the optimization sense to the provided value.
setOptimizationSense(OptSense) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Sets the optimization sense.
setParamFile(String) - Method in class sbrt.ext.cplex.CplexSolver
Reads the program solver parameter file with the provided name.
setParamFile(String) - Method in class sbrt.ext.glpk.GlpkSolver
Throws UnsupportedOperationException.
setParamFile(String) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Reads the program solver parameter file with the provided name.
setPIntercept(double) - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Sets the value of the positioning variables at the edges of the convex polytope.
setPoint(Map<? extends V, Double>) - Method in class sbrt.kernel.math.geom.comp.CdHarComp
Sets the initial point.
setPoint(Map<? extends V, Double>) - Method in class sbrt.kernel.math.geom.proc.CdHarProcess
Sets the initial point.
setPointsPerPoint(int) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Sets the number of points to generate for each point added to the specified results manager.
setPointsPerPoint(int) - Method in class sbrt.kernel.fba.proc.CdHarFluxVectorProcess
Sets the number of points to generate for each point added to the specified results manager.
setPointsPerPoint(int) - Method in class sbrt.kernel.math.geom.proc.CdHarProcess
Sets the total number of points to generate for each point added to the provided results manager.
setRandom(Random) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Sets the random number generator.
setRandom(Random) - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Sets the random number generator to the one provided.
setRandom(Random) - Method in class sbrt.kernel.fba.proc.RandomObjectiveGenerator
Sets the random number generator to the one provided.
setRandom(Random) - Method in class sbrt.kernel.math.geom.comp.CdHarComp
Sets the random number generator.
setRandom(Random) - Method in class sbrt.kernel.math.geom.proc.CdHarProcess
Sets the random number generator.
setReactionNames(Collection<String>) - Method in class sbrt.kernel.fba.proc.CvFluxIntervalProcess
Sets the names of reactions for which flux intervals are to be computed.
setReactionNames(Set<String>) - Method in class sbrt.kernel.fba.proc.FluxIntervalProcess
Sets the names of reactions for which flux ranges are to be computed.
setReactions(Set<String>) - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Sets the reaction names for which random constraints are to be generated.
setRevConstraint(Interval) - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Sets the constraint used for active reversible reactions.
setReverseSuffix(String) - Method in class sbrt.kernel.fba.proc.RevRxnBreakerProcess
Sets the reverse suffix if a non-default value is desired.
setRowConstraint(T, Interval) - Method in class sbrt.ext.cplex.CplexSolver
Sets the constraint for the provided row variable.
setRowConstraint(X, Interval) - Method in class sbrt.ext.glpk.GlpkSolver
Sets the constraint for the provided row variable.
setRowConstraint(Object, Interval) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Changes the constraint of the provided row variable.
setRowConstraint(X, Interval) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Sets the constraint for the provided row variable.
setRowConstraints(Map<? extends R, Interval>) - Method in class sbrt.ext.cplex.CplexSolver
Sets the constraints for the provided row variables.
setRowConstraints(Map<? extends R, Interval>) - Method in class sbrt.ext.glpk.GlpkSolver
Sets the constraints for the provided row variables.
setRowConstraints(Map<?, Interval>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Changes the constraints on more than one row variable.
setRowConstraints(Map<? extends R, Interval>) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Sets the constraints for the provided row variables.
setRxnDeletionSource(Iterable<Set<String>>) - Method in class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Sets the reaction deletion input source.
setRxnDeletionSource(Iterable<Set<String>>) - Method in class sbrt.kernel.fba.proc.RxnDeletionProcess
Sets the reaction deletion input source.
setRxnExprConstraint(MathExpr<String>, Interval) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Changes the constraint on the provided mathematical expression of fluxes.
setRxnExprConstraint(MathExpr<String>, Interval) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Changes the constraint on the provided mathematical expression of fluxes.
setRxnExprConstraint(LinearComb<String>, Interval) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Changes the constraint on the provided linear combination of fluxes.
setRxnExprConstraint(MathExpr<String>, Interval) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Changes the constraint on the provided mathematical expression of fluxes.
setRxnExprConstraint(MathExpr<String>, Interval) - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Changes the constraint on the provided mathematical expression of fluxes.
setRxnExprConstraint(MathExpr<String>, Interval) - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Changes the constraint on the provided mathematical expression of fluxes.
setRxnExprConstraint(MathExpr<String>, Interval) - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Changes the constraint on the provided mathematical expression of fluxes.
setRxnExprConstraints(Map<? extends MathExpr<String>, Interval>) - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Changes the constraints on more than one mathematical expression of fluxes.
setRxnExprConstraints(Map<? extends MathExpr<String>, Interval>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Changes the constraints on more than one mathematical expression of fluxes.
setRxnExprConstraints(Map<? extends MathExpr<String>, Interval>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Changes the constraints on more than one mathematical expression of fluxes.
setRxnExprConstraints(Map<? extends MathExpr<String>, Interval>) - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Changes the constraints on more than one mathematical expression of fluxes.
setRxnExprConstraints(Map<? extends MathExpr<String>, Interval>) - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Changes the constraints on more than one mathematical expression of fluxes.
setRxns(Map<String, ? extends ChemRxn>) - Method in class sbrt.kernel.fba.proc.RevRxnBreakerProcess
Sets the reactions for which reversible reactions will be broken.
SETS_FILE - Static variable in class sbrt.shell.mng.comb.SingleElementUnionManager
The keyword used to denote the name of the file containing the collection of sets.
setSafetyLevel(int) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Sets the safety level.
setSampleA(List<? extends Number>) - Method in class sbrt.kernel.math.stat.proc.MwUAnalysis
Sets sample A to the provided list of numbers.
setSampleB(List<? extends Number>) - Method in class sbrt.kernel.math.stat.proc.MwUAnalysis
Sets sample B to the provided list of numbers.
setSets(Collection<Set<E>>) - Method in class sbrt.kernel.math.comb.proc.SingleElementUnionProc
Sets the collection of sets to that provided.
setSets(Collection<Set<E>>) - Method in class sbrt.kernel.math.comb.proc.StrictSingleElementUnionProc
Sets the collection of sets to that provided.
setSinkSuffix(String) - Method in class sbrt.kernel.fba.proc.RevRxnBreakerProcess
Sets the sink suffix if a non-default value is desired.
setSolver(LinearSystemSolver<String>) - Method in class sbrt.kernel.fba.proc.FbaSolverProcess
Sets the linear system solver to be used.
setSolver(LinearSystemSolver<V>) - Method in class sbrt.kernel.math.algebra.proc.LinearSolverProcess
Sets the linear system solver.
setSourceSuffix(String) - Method in class sbrt.kernel.fba.proc.RevRxnBreakerProcess
Sets the source suffix if a non-default value is desired.
setTolerance(double) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Sets the constraint tolerance.
setTolerance(double) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Sets the constraint tolerance.
setTolerance(double) - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Sets the constraint tolerance.
setTolerance(double) - Method in class sbrt.kernel.utilities.proc.IntervalComparison
Sets the equivalence tolerance.
setTolerance(double) - Method in class sbrt.kernel.utilities.proc.VectorComparison
Sets the equivalence tolerance.
setTotal(int) - Method in class sbrt.kernel.utilities.PercentProgressMonitor
Sets the total number of times increment() can be called.
setVectorSource(Iterator<Map<K, V>>) - Method in class sbrt.kernel.math.algebra.proc.VectorIntersection
Sets the vector source.
setVectorSource(Iterable<Map<V, Double>>) - Method in class sbrt.kernel.utilities.proc.VectorComparison
Sets of the source of numerical vectors.
setXValues(Map<? extends V, Double>) - Method in class sbrt.kernel.math.stat.proc.CorrelationAnalysis
Sets the x values.
setXValues(Map<? extends V, Double>) - Method in class sbrt.kernel.math.stat.proc.MultipleCorrelationAnalysis
Sets the x values.
setYValues(Map<? extends V, Double>) - Method in class sbrt.kernel.math.stat.proc.CorrelationAnalysis
Sets the y values.
setYValues(Iterable<Map<V, Double>>) - Method in class sbrt.kernel.math.stat.proc.MultipleCorrelationAnalysis
Sets the source of y values.
setZeroCutoff(double) - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Sets the zero cutoff.
setZeroCutoff(double) - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Sets the zero cutoff to the provided value.
setZeroCutoff(double) - Method in class sbrt.kernel.fba.proc.CatalystDeletionProcess
Sets the zero cutoff to the provided value.
setZeroCutoff(double) - Method in class sbrt.kernel.fba.proc.CvCatalystDeletionProcess
Sets the zero cutoff to the provided value.
setZeroCutoff(double) - Method in class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Sets the zero cutoff to the provided value.
setZeroCutoff(double) - Method in class sbrt.kernel.fba.proc.FluxActivityProcess
Sets the zero cutoff to the provided value.
setZeroCutoff(double) - Method in class sbrt.kernel.fba.proc.FluxPlasticityProcess
Sets the zero cutoff to the provided value.
setZeroCutoff(double) - Method in class sbrt.kernel.fba.proc.RxnDeletionProcess
Sets the zero cutoff to the provided value.
SfoofSource<F extends Fluxome> - Class in sbrt.shell.io.fba
This class is used to provide a source of serialized FBA optimization output files.
SfoofSource(Iterator<String>, FileFormat, Set<String>, FbaOptFileLineFormat) - Constructor for class sbrt.shell.io.fba.SfoofSource
Constructs a new source of serialized FBA optimization output files.
SfoofSource(Iterator<String>, String, FileFormat, Set<String>, FbaOptFileLineFormat) - Constructor for class sbrt.shell.io.fba.SfoofSource
Constructs a new source of serialized FBA optimization output files.
ShellProcessManager<K,V> - Interface in sbrt.shell.mng
This interface is used to represent shell process managers.
SimpleFluxIntervalComputer<F extends Fluxome> - Class in sbrt.kernel.fba.comp
This class is used to compute flux intervals in the simplest possible way.
SimpleFluxIntervalComputer(FbaOptimizer<F>, double) - Constructor for class sbrt.kernel.fba.comp.SimpleFluxIntervalComputer
Constructs a new flux interval computer.
SimpleFluxIntervalManager - Class in sbrt.shell.mng.fba
This class is used to manage simple flux interval processes.
SimpleFluxIntervalManager() - Constructor for class sbrt.shell.mng.fba.SimpleFluxIntervalManager
 
SimpleFormat<T> - Interface in sbrt.shell.text
This interface is used to represent simple formats.
SimpleListFormat<E> - Class in sbrt.shell.text
This interface is used to wrap ListFormat objects as SimpleFormat objects.
SimpleListFormat(ListFormat<E>) - Constructor for class sbrt.shell.text.SimpleListFormat
Constructs a new simple list format from the provided list format.
SimpleRxnFileReader - Class in sbrt.shell.proc.fba
This class is used to translate simple reaction files from, say, spreadsheets into FBA Reaction Files.
SimpleRxnFileReader() - Constructor for class sbrt.shell.proc.fba.SimpleRxnFileReader
Constructs a new simple reaction file reader.
SimpleRxnFileTransManager - Class in sbrt.shell.mng.fba
This class is used to manage the translation of simple reaction files into Systems Biology Research Tool (SBRT) FBA Reaction Files.
SimpleRxnFileTransManager() - Constructor for class sbrt.shell.mng.fba.SimpleRxnFileTransManager
 
SimpleSetFormat<E> - Class in sbrt.shell.text
This interface is used to wrap ListFormat objects as SimpleFormat objects.
SimpleSetFormat(LinkedHashSetFormat<E>) - Constructor for class sbrt.shell.text.SimpleSetFormat
Constructs a new simple set format from the provided set format.
simplify(LinearSystemSolution<V>, Map<? extends V, Interval>, double) - Static method in class sbrt.kernel.math.algebra.HashLinearSystemSolution
Returns a simplified version of the provided linear system solution given the variable bounds.
simplify(Map<?, Double>, double) - Method in class sbrt.kernel.math.algebra.HashLinearSystemSolution
Computes and returns a simplified solution by plugging in the provided values.
simplify(Map<?, Double>, double) - Method in interface sbrt.kernel.math.algebra.LinearSystemSolution
Computes and returns a simplified solution by plugging in the provided values.
SingleElementUnionManager - Class in sbrt.shell.mng.comb
This class is used to manage single-element union computers.
SingleElementUnionManager() - Constructor for class sbrt.shell.mng.comb.SingleElementUnionManager
 
SingleElementUnionProc<E> - Class in sbrt.kernel.math.comb.proc
This class is used to wrap the single element union computer as a process.
SingleElementUnionProc() - Constructor for class sbrt.kernel.math.comb.proc.SingleElementUnionProc
Constructs a new single-element union process.
SingleElementUnionsV1 - Class in sbrt.kernel.math.comb.comp
This class is used to compute the single-element unions of collections of sets.
SingleElementUnionsV1() - Constructor for class sbrt.kernel.math.comb.comp.SingleElementUnionsV1
 
SingleElementUnionsV2 - Class in sbrt.kernel.math.comb.comp
This class is used to compute the single-element unions of collections of sets.
SingleElementUnionsV2() - Constructor for class sbrt.kernel.math.comb.comp.SingleElementUnionsV2
 
SingleRm<R> - Class in sbrt.kernel.io
This class is used to store a single result that can be easily retrieved.
SingleRm() - Constructor for class sbrt.kernel.io.SingleRm
 
singleTerm(V, double) - Static method in class sbrt.kernel.math.HashLinearComb
Returns a single-term linear combination with the provided variable and coefficient.
singleTerm(V, double, double) - Static method in class sbrt.kernel.math.HashLinearComb
Returns a single-term linear combination with the provided variable, coefficient, and zero cutoff.
singleTerm(double, V) - Static method in class sbrt.kernel.math.HashLinearComb
Returns a single-term linear combination with the provided variable and coefficient.
singleTerm(V) - Static method in class sbrt.kernel.math.HashLinearComb
Returns a single-term linear combination with the provided variable.
singleTerm(LinearComb.Term<V>) - Static method in class sbrt.kernel.math.HashLinearComb
Returns a single-term linear combination with the provided term.
SingleVectorConverterManager - Class in sbrt.shell.mng.algebra
This class is used to convert multiple files containing single vectors into a single file containing multiple vectors.
SingleVectorConverterManager() - Constructor for class sbrt.shell.mng.algebra.SingleVectorConverterManager
 
SINK_SUFFIX - Static variable in class sbrt.kernel.fba.proc.RevRxnBreakerProcess
The default suffix added to the names or IDs of sink reactions.
SinkRxn - Class in sbrt.kernel.fba
This class is used to represent exchange reactions that transport chemicals from a chemical system to its surroundings.
SinkRxn(String) - Constructor for class sbrt.kernel.fba.SinkRxn
Constructs a new sink reaction for the provided chemical species.
sinkRxns() - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the total number of sink reactions contained in this fluxome.
sinkRxns() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the total number of sink reactions contained in this fluxome.
size() - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.size().
size() - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.size().
size() - Method in class sbrt.kernel.utilities.UnmodifiableMap
See Map.size().
size() - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.size().
SlpCycleComputer - Class in sbrt.kernel.fba.comp
This class is used to identify the steady state cycles in stoichiometric networks.
SlpCycleComputer(ExtremeCurrentComputer) - Constructor for class sbrt.kernel.fba.comp.SlpCycleComputer
Constructs a new steady state cycle computer from the given extreme current computer.
SlpCycleIdManager - Class in sbrt.shell.mng.fba
This class is used to manage steady state cycle identification.
SlpCycleIdManager() - Constructor for class sbrt.shell.mng.fba.SlpCycleIdManager
 
SlpExCurrComputerV2 - Class in sbrt.kernel.fba.comp
This class is an implementation of an algorithm for identifying extreme currents in stoichiometric networks.
SlpExCurrComputerV2() - Constructor for class sbrt.kernel.fba.comp.SlpExCurrComputerV2
Constructs a new extreme current computer.
SmdMatrix<R,C> - Interface in sbrt.kernel.math.algebra
This interface is used to represent sparse mutable matrices containing strictly double precision numbers as elements.
SmoFile<K,V> - Class in sbrt.shell.io
This class is used to write serialized maps to output files.
SmoFile(String, FileFormat, Set<? extends K>) - Constructor for class sbrt.shell.io.SmoFile
Constructs a new serialized map output file from the provided arguments.
SmoFileSource<K,V> - Class in sbrt.shell.io
This class is used to provided a source of serialized map output files.
SmoFileSource(Iterator<String>, FileFormat, Set<? extends K>) - Constructor for class sbrt.shell.io.SmoFileSource
Constructs a new source of serialized map output files.
solve(Map<LinearComb<V>, Double>) - Method in class sbrt.ext.mma.algebra.MathematicaSolver
Computes and returns a solution to the provided system of linear equations.
solve(Fluxome, LinearSystemSolver<String>) - Static method in class sbrt.kernel.fba.comp.FbaSolver
Solves Sv = 0, where S is the stoichiometry matrix of the provided fluxome and v is the vector of fluxes.
solve(Map<LinearComb<V>, Double>) - Method in interface sbrt.kernel.math.algebra.LinearSystemSolver
Computes and returns a solution to the provided system of linear equations.
solveFor(Object, double) - Method in class sbrt.kernel.math.HashLinearComb
Equates this linear combination to the provided constant and solves for the provided variable.
solveFor(Object, double) - Method in interface sbrt.kernel.math.LinearComb
Equates this linear combination to the provided constant and solves for the provided variable.
SOLVER - Static variable in class sbrt.shell.ProgramSolverFactory
The keyword used to denote the name of a program solver.
SOURCE_SUFFIX - Static variable in class sbrt.kernel.fba.proc.RevRxnBreakerProcess
The default suffix added to the names or IDs of source reactions.
SourceRxn - Class in sbrt.kernel.fba
This class is used to represent exchange reactions that transport chemicals to a chemical system from its surroundings.
SourceRxn(String) - Constructor for class sbrt.kernel.fba.SourceRxn
Constructs a new source for the provided chemical species.
sourceRxns() - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the total number of source reactions contained in this fluxome.
sourceRxns() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the total number of source reactions contained in this fluxome.
SparseDoubleMatrix<R,C> - Interface in sbrt.kernel.math.algebra
This interface is used to represent sparse matrices whose elements are strictly double precision numbers.
SparseDoubleMatrixWrap<R,C> - Class in sbrt.kernel.math.algebra
This class is used to wrap mutable matrices as an immutable SparseDoubleMatrix.
SparseDoubleMatrixWrap(SparseDoubleMatrix<R, C>) - Constructor for class sbrt.kernel.math.algebra.SparseDoubleMatrixWrap
Constructs a new wrapper around the provided matrix.
SPEARMANS_RHO - Static variable in class sbrt.shell.mng.stat.CorrelationManager
The value used to denote a Spearman's rho correlation coefficient.
SpecialChars - Class in sbrt.shell.text
This class contains a set of characters that could be considered as special in some situations.
species() - Method in interface sbrt.kernel.fba.Fluxome
Returns the total number of chemical species contained in this fluxome.
species() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the total number of chemical species contained in this fluxome.
species() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the total number of chemical species contained in this fluxome.
start() - Method in class sbrt.kernel.utilities.AbstractProgressMonitor
Causes this progress monitor to start monitoring a duration of time.
start() - Method in interface sbrt.kernel.utilities.MutableProgressMonitor
Causes this progress monitor to start monitoring a duration of time.
started() - Method in class sbrt.kernel.utilities.AbstractProgressMonitor
Indicates if this progress monitor has already been started.
started() - Method in interface sbrt.kernel.utilities.ProgressMonitor
Indicates if this progress monitor has already been started.
startR() - Static method in class sbrt.ext.R.R
Starts the R engine if it is not already running.
startR(PrintWriter) - Static method in class sbrt.shell.mng.stat.CorrelationManager
Starts the R engine and writes an informative message to the provided print writer.
stop() - Method in class sbrt.kernel.utilities.AbstractProgressMonitor
Causes this progress monitor to stop monitoring a duration of time.
stop() - Method in interface sbrt.kernel.utilities.MutableProgressMonitor
Causes this progress monitor to stop monitoring a duration of time.
stopped() - Method in class sbrt.kernel.utilities.AbstractProgressMonitor
Indicates if this progress monitor has already been stopped.
stopped() - Method in interface sbrt.kernel.utilities.ProgressMonitor
Indicates if this progress monitor has already been stopped.
StrictSingleElementUnionManager - Class in sbrt.shell.mng.comb
This class is used to manage single-element union computers.
StrictSingleElementUnionManager() - Constructor for class sbrt.shell.mng.comb.StrictSingleElementUnionManager
 
StrictSingleElementUnionProc<E> - Class in sbrt.kernel.math.comb.proc
This class is used to wrap the strict single-element union computer as a process.
StrictSingleElementUnionProc() - Constructor for class sbrt.kernel.math.comb.proc.StrictSingleElementUnionProc
Constructs a new strict single-element union process.
StrictSingleElementUnions - Class in sbrt.kernel.math.comb.comp
This class is used to compute the single-element unions of collections of sets.
StrictSingleElementUnions() - Constructor for class sbrt.kernel.math.comb.comp.StrictSingleElementUnions
Constructs a new strict single-element union computer.
StringFormat - Class in sbrt.shell.text
This class is used to define a format for String objects.
StringFormat() - Constructor for class sbrt.shell.text.StringFormat
 
subList(int, int) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.subList(int, int).
successors(Object) - Method in class sbrt.kernel.math.graph_theory.DirectedGraph
Returns the number of successors of the provided node.
SURR - Static variable in class sbrt.shell.proc.fba.MetatoolInputWriter
The string used to denote the surroundings.
SURR - Static variable in class sbrt.shell.text.fba.IrrevRxnFormatV1
The string used to denote the surroundings.
SURR - Static variable in class sbrt.shell.text.fba.IrrevRxnFormatV2
The string used to denote the surroundings.
SURR - Static variable in class sbrt.shell.text.fba.RevRxnFormatV1
The string used to denote the surroundings.
SURR - Static variable in class sbrt.shell.text.fba.RevRxnFormatV2
The string used to denote the surroundings.
SvCdHarFluxVectorProcess<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to perform space variation coordinate direction hit-and-run flux vector processes.
SvCdHarFluxVectorProcess(CdHarFluxComp<F>) - Constructor for class sbrt.kernel.fba.proc.SvCdHarFluxVectorProcess
Constructs a new flux space variation coordinate direction hit-and-run flux vector process.
SvInitialPointProcess<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to perform flux space variation initial point processes.
SvInitialPointProcess(InitialPointComputer<F>) - Constructor for class sbrt.kernel.fba.proc.SvInitialPointProcess
Constructs a new constraint variation initial point process.
SYSTEM_SOLUTION_FILE - Static variable in class sbrt.shell.mng.fba.FbaManager
The keyword used to denote a file containing a solution to the system of linear equations formed by a fluxome.

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