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

G

GENE_FILE_NAME - Static variable in class sbrt.shell.mng.fba.BiggSbmlReaderManager
Used to denote the name of the file to which gene-reaction relationships should be written.
GENE_FILE_NAME - Static variable in class sbrt.shell.mng.fba.PalssonSbmlReaderManager
Used to denote the name of the file to which gene-reaction relationships should be written.
get(int) - Method in class sbrt.kernel.math.graph_theory.Path
Returns the node at the specified position in this path.
get(int) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.get(int).
get(Object) - Method in class sbrt.kernel.utilities.UnmodifiableMap
See Map.get(Object).
get() - Static method in class sbrt.shell.HomeDirectory
Returns the SBRT's home directory.
get() - Static method in class sbrt.shell.io.DevNull
Returns an instance of this class.
get() - Static method in class sbrt.shell.io.EndOfFile
Returns an instance of this class.
get() - Static method in class sbrt.shell.WorkingDirectory
Returns the current working directory.
getActiveFluxes() - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Returns the number of active fluxes in each set of randomly generated flux constraints.
getAlwaysActive(Map<String, Interval>, double) - Method in class sbrt.kernel.fba.analysis.FluxIntervalAnalyzer
Returns the always-active fluxes in the provided map.
getAlwaysActive() - Method in class sbrt.kernel.fba.proc.FluxPlasticityProcess.Results
Returns the set of fluxes that are always active.
getApproxT() - Method in class sbrt.kernel.math.stat.comp.MannWhitneyResults
Returns the t value approximated from the computed U statistic.
getApproxZ(Map<? extends V, Double>, Map<? extends V, Double>) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns a Z approximation for the provided values.
getApproxZ(Collection<Double>, Collection<Double>) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns a Z approximation for the provided values.
getApproxZ(double[], double[]) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns a Z approximation for the provided values.
getApproxZ() - Method in class sbrt.kernel.math.stat.comp.TauResult
Returns the Z value approximated from the computed correlation statistic.
getArray(Collection<? extends Number>) - Static method in class sbrt.kernel.utilities.Util
Returns an array containing the values in the provided collection as doubles.
getArray(Collection<Integer>) - Static method in class sbrt.kernel.utilities.Util
Returns an array containing the values in the provided collection.
getArray() - Static method in class sbrt.shell.text.SpecialChars
Returns an array of the characters contained in this class.
getArrays(Map<?, Double>, Map<?, Double>) - Static method in class sbrt.kernel.utilities.Util
Returns a 2 x n array containing the values from the provided maps.
getBasic(String) - Static method in class sbrt.shell.io.TextInputFile
Returns a basic text input file.
getBasic(String, FileFormat) - Static method in class sbrt.shell.io.TextInputFile
Returns a basic text input file.
getBasic(String) - Static method in class sbrt.shell.io.TextOutputFile
Returns a basic text output file.
getBasic(String, FileFormat) - Static method in class sbrt.shell.io.TextOutputFile
Returns a basic text output file with the provided file format.
getBasic() - Static method in class sbrt.shell.text.AmpersandSetFormat
Returns a AmpersandSetFormat that does not format or parse the elements supplied to it.
getBasic() - Static method in class sbrt.shell.text.BoolRelFormatV1
Returns an BoolRelFormatV1 that does not format or parse the elements supplied to it.
getBasic() - Static method in class sbrt.shell.text.ColonMapEntryFormatV1
Returns a ColonMapEntryFormatV1 that does not format or parse the keys or values supplied to it.
getBasic() - Static method in class sbrt.shell.text.ColonMapFormatV1
Returns a ColonMapFormatV1 that does not format or parse the keys or values supplied to it.
getBasic() - Static method in class sbrt.shell.text.EqualsMapEntryFormatV1
Returns an EqualsMapEntryFormatV1 that does not format or parse the keys or values supplied to it.
getBasic() - Static method in class sbrt.shell.text.EqualsMapFormatV1
Returns an EqualsMapFormatV1 that does not format or parse the keys or values supplied to it.
getBasic() - Static method in class sbrt.shell.text.math.DirEdgeFormatV1
Returns a DirEdgeFormatV1 that does not format or parse the nodes of the edges supplied to it.
getBasic() - Static method in class sbrt.shell.text.math.LinearCombFormatV1
Returns a LinearCombFormatV1 that does not format or parse the variables supplied to it.
getBasic() - Static method in class sbrt.shell.text.math.LinearCombFormatV2
Returns a LinearCombFormatV1 that does not format or parse the variables supplied to it.
getBasic() - Static method in class sbrt.shell.text.PipeListFormat
Returns a PipeListFormat that does not format or parse the elements supplied to it.
getBasic() - Static method in class sbrt.shell.text.PipeSetFormat
Returns a PipeSetFormat that does not format or parse the elements supplied to it.
getBasic() - Static method in class sbrt.shell.text.TabListFormat
Returns a TabListFormat that does not format or parse the elements supplied to it.
getBasic() - Static method in class sbrt.shell.text.TabSetFormat
Returns a TabSetFormat that does not format or parse the elements supplied to it.
getBasic() - Static method in class sbrt.shell.text.WhitespaceListFormat
Returns a WhitespaceListFormat that does not format or parse the elements supplied to it.
getBasic() - Static method in class sbrt.shell.text.WhitespaceSetFormat
Returns a WhitespaceSetFormat that does not format or parse the elements supplied to it.
getBoundedMax(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Computes the maximum value of the provided objective function.
getBoundedMax(String) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Computes the maximum flux of the reaction with the provided name.
getBoundedMaxWithRxnsMinimized(String, Set<String>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Computes the maximum flux of the reaction with the provided name while constraining the fluxes of the provided reactions to their minimum.
getBoundedMin(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Computes the minimum value of the provided objective function.
getBoundedMin(String) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Computes the minimum flux of the reaction with the provided name.
getBoundingPlanes() - Method in interface sbrt.kernel.math.geom.ConvexPolytope
Returns the set of bounding hyperplanes that define this convex polytope.
getBoundingPlanes() - Method in class sbrt.kernel.math.geom.HashConvexPolytope
Returns the set of bounding hyperplanes that define this convex polytope.
getBounds() - Method in exception sbrt.kernel.math.ConstraintViolationException
Returns the constraints that have been violated.
getBounds() - Method in class sbrt.kernel.math.geom.ParallelHyperplanes
Returns the bounding values used to define the inequality.
getCanonicalName() - Method in class sbrt.shell.io.AbstractMapInputFile
Returns the canonical name of this file.
getCanonicalName() - Method in class sbrt.shell.io.AbstractMapOutputFile
Returns the canonical name of this file.
getCanonicalName(String) - Static method in class sbrt.shell.io.AbstractSbrtFile
Returns the canonical name of the specified file.
getCanonicalName() - Method in class sbrt.shell.io.fba.ColumnOrFbaOptOutputFile
Returns the canonical name of this file.
getCanonicalName() - Method in class sbrt.shell.io.fba.FluxCapInputFile
Returns the canonical name of this file.
getCanonicalName() - Method in class sbrt.shell.io.fba.FluxIntervalInputFile
Returns the canonical name of this file.
getCanonicalName() - Method in class sbrt.shell.io.fba.RowOrFbaOptOutputFile
Returns the canonical name of this file.
getCanonicalName() - Method in class sbrt.shell.io.fba.SerFbaOptOutputFile
Returns the canonical name of this file.
getCanonicalName() - Method in interface sbrt.shell.io.SbrtFile
Returns the canonical name of this file.
getCanonicalName() - Method in class sbrt.shell.io.SerializedInputFile
Returns the canonical name of this file.
getCanonicalName() - Method in class sbrt.shell.io.SerializedOutputFile
Returns the canonical name of this file.
getCanonicalName() - Method in class sbrt.shell.io.TextInputFile
Returns the canonical name of this file.
getCanonicalName() - Method in class sbrt.shell.io.TextOutputFile
Returns the canonical name of this file.
getCat() - Method in class sbrt.shell.proc.fba.MetatoolInputReader.Results
Returns the reactions that are listed in the -CAT section of the input file.
getCatalystRule(String) - Method in interface sbrt.kernel.fba.CatalyzedFluxome
Returns the boolean logic rule for catalysts of the reaction with the provided name.
getCatalystRule(String) - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the boolean logic statement for the catalysts of the reaction with the provided name.
getCatalystRule(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the boolean logic statement for the catalysts of the reaction with the provided name.
getCatalystRule(String) - Method in interface sbrt.kernel.fba.MixedFluxome
Returns the boolean logic statement for the catalysts of the reaction with the provided name.
getCatalystRule(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the boolean logic statement for the catalysts of the reaction with the provided name.
getCatalystRules() - Method in interface sbrt.kernel.fba.CatalyzedFluxome
Returns the boolean logic rules for the catalysts of all reactions in this fluxome.
getCatalystRules() - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns all of the boolean logic statements regarding reaction catalysis.
getCatalystRules() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns all of the boolean logic statements regarding reaction catalysis.
getCatalystRules() - Method in interface sbrt.kernel.fba.MixedFluxome
Returns all of the boolean logic statements regarding reaction catalysis.
getCatalystRules() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns all of the boolean logic statements regarding reaction catalysis.
getCatalystRxnAssoc() - Method in class sbrt.kernel.fba.proc.NetworkInfoProcess.Results
Returns the catalyst-reaction associations contained in the fluxome.
getCatalysts() - Method in interface sbrt.kernel.fba.CatalyzedFluxome
Returns the set of all catalysts contained in this fluxome.
getCatalysts() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the set of names of all catalysts contained in this fluxome.
getCatalysts() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the set of names of all catalysts contained in this fluxome.
getCatalysts() - Method in class sbrt.kernel.fba.proc.NetworkInfoProcess.Results
Returns the catalysts contained in the fluxome.
getCatalysts(Fluxome, String) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns the reaction-catalyst associations contained in the file with the provided name.
getCatalysts(Fluxome, String, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns the reaction-catalyst associations contained in the file with the provided name.
getCatalysts(Node, String) - Method in class sbrt.shell.text.fba.BiggRxnNodeParser
Returns the boolean logic rules for the catalysts of the provided reaction node.
getCatalysts(Node, String) - Method in class sbrt.shell.text.fba.PalssonRxnNodeParser
Returns the boolean logic rules for the catalysts of the provided reaction node.
getCatalyzedRxnNames(String) - Method in interface sbrt.kernel.fba.CatalyzedFluxome
Returns the set of names of all chemical reactions contained in this fluxome that are catalyzed by the provided catalyst.
getCatalyzedRxnNames(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the names of the reactions catalyzed by the provided catalyst.
getCatalyzedRxnNames(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the names of the reactions catalyzed by the provided catalyst.
getCatalyzedRxns(String) - Method in interface sbrt.kernel.fba.CatalyzedFluxome
Returns the chemical reactions contained in this fluxome that are catalyzed by the provided catalyst.
getCatalyzedRxns(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns all of the internal reactions contained in this fluxome that are catalyzed by the provided catalyst.
getCatalyzedRxns(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns all of the internal reactions contained in this fluxome that are catalyzed by the provided catalyst.
getCause() - Method in exception sbrt.ext.mma.MathematicaException
Returns the MathLinkException responsible for this exception.
getChangedVariables() - Method in class sbrt.kernel.math.geom.comp.CdHarComp.Results
Returns the variables whose values are different than they were in the previous point.
getChemSpecies() - Method in class sbrt.kernel.fba.proc.NetworkInfoProcess.Results
Returns the metabolites contained in the fluxome.
getChemSpeciesFormat() - Method in class sbrt.shell.text.chem.IrrevRxnFormatV1
Returns the format used for chemical species.
getChemSpeciesFormat() - Method in class sbrt.shell.text.chem.RevRxnFormatV1
Returns the format used for chemical species.
getChemSpeciesFormat() - Method in class sbrt.shell.text.fba.IrrevRxnFormatV1
Returns the format used for chemical species.
getChemSpeciesFormat() - Method in class sbrt.shell.text.fba.IrrevRxnFormatV2
Returns the format used for chemical species.
getChemSpeciesFormat() - Method in class sbrt.shell.text.fba.RevRxnFormatV1
Returns the format used for chemical species.
getChemSpeciesFormat() - Method in class sbrt.shell.text.fba.RevRxnFormatV2
Returns the format used for chemical species.
getChemSpeciesFormat() - Method in class sbrt.shell.text.fba.RxnFormatV1
Returns the format used for chemical species.
getCoeff() - Method in class sbrt.ext.R.stat.RCorrelator.Result
Returns the computed correlation coefficient.
getCoeff() - Method in interface sbrt.kernel.math.stat.comp.CorrResult
Returns the computed correlation coefficient.
getCoeff() - Method in class sbrt.kernel.math.stat.comp.TauResult
Returns the computed correlation statistic.
getCoeffFormat() - Method in class sbrt.shell.text.math.LinCombTermFormatV1
Returns the format used for coefficients.
getCoeffFormat() - Method in class sbrt.shell.text.math.LinCombTermFormatV2
Returns the format used for coefficients.
getCoeffFormat() - Method in class sbrt.shell.text.math.LinearCombFormatV1
Returns the format used for coefficients.
getCoeffFormat() - Method in class sbrt.shell.text.math.LinearCombFormatV2
Returns the format used for coefficients.
getCoefficient() - Method in class sbrt.kernel.math.AbstractLinearComb.Term
Returns the coefficient of this term.
getCoefficient(Object) - Method in class sbrt.kernel.math.HashLinearComb
Returns the coefficient of the term containing the provided variable.
getCoefficient(Object) - Method in interface sbrt.kernel.math.LinearComb
Returns the coefficient of the term containing the provided variable.
getCoefficient() - Method in interface sbrt.kernel.math.Polynomial.Term
Returns the coefficient of this term.
getColExprConstraint(MathExpr<?>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the current constraint on the provided expression.
getColExprConstraints() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns all current constraints on mathematical expressions of column variables.
getColExprs() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the set of all mathematical expressions of column variables.
getColIndNzEl(Object) - Method in class sbrt.kernel.math.algebra.HashMatrix
Returns the set of column indices whose elements are nonzero in the row corresponding to the provided index.
getColIndNzEl(Object) - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Returns the set of column indices whose elements are nonzero in the row corresponding to the provided index.
getColIndNzEl(Object) - Method in interface sbrt.kernel.math.algebra.SparseDoubleMatrix
Returns the set of column indices whose elements are nonzero in the row corresponding to the provided index.
getColIndNzEl(Object) - Method in class sbrt.kernel.math.algebra.SparseDoubleMatrixWrap
Returns the set of column indices whose elements are nonzero in the row corresponding to the provided index.
getColIndNzEl(Object) - Method in class sbrt.kernel.math.algebra.TreeMatrix
Returns the set of column indices whose elements are nonzero in the row corresponding to the provided index.
getColumn(Object) - Method in interface sbrt.kernel.math.algebra.DoubleMatrix
Returns the column corresponding to the provided column index.
getColumn(Object) - Method in class sbrt.kernel.math.algebra.DoubleMatrixWrap
Returns the column corresponding to the provided column index.
getColumn(Object) - Method in class sbrt.kernel.math.algebra.HashMatrix
Returns the column corresponding to the provided column index.
getColumn(Object) - Method in interface sbrt.kernel.math.algebra.Matrix
Returns the column corresponding to the provided column index.
getColumn(Object) - Method in class sbrt.kernel.math.algebra.MatrixWrap
Returns the column corresponding to the provided column index.
getColumn(Object) - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Returns the column corresponding to the provided column index.
getColumn(Object) - Method in interface sbrt.kernel.math.algebra.SparseDoubleMatrix
Returns the column corresponding to the provided column index.
getColumn(Object) - Method in class sbrt.kernel.math.algebra.SparseDoubleMatrixWrap
Returns the column corresponding to the provided column index.
getColumn(Object) - Method in class sbrt.kernel.math.algebra.TreeMatrix
Returns the column corresponding to the provided column index.
getColumnConstraint(Object) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the current constraint on the provided column variable.
getColumnConstraints() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the current constraints for each column variable in the program matrix.
getColumnHeaders() - Method in class sbrt.shell.io.fba.ColumnOrFbaOptOutputFile
Returns the set of column headers that are written to this file.
getColumnIndex() - Method in class sbrt.kernel.math.algebra.IndexPair
Returns the column index.
getColumnIndex() - Method in class sbrt.kernel.math.algebra.MatrixElement
Returns the column index of this matrix element.
getColumnIndexFormat() - Method in class sbrt.shell.text.math.IndexPairFormatV1
Returns the format used for column indices.
getColumnIndices() - Method in class sbrt.kernel.math.algebra.HashMatrix
Returns the set of column indices contained in this matrix.
getColumnIndices() - Method in interface sbrt.kernel.math.algebra.Matrix
Returns the set of column indices contained in this matrix.
getColumnIndices() - Method in class sbrt.kernel.math.algebra.MatrixWrap
Returns the set of column indices contained in this matrix.
getColumnIndices() - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Returns the set of column indices contained in this matrix.
getColumnIndices() - Method in class sbrt.kernel.math.algebra.TreeMatrix
Returns the set of column indices contained in this matrix.
getColumnMax(Object) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Computes the maximum value of the provided column variable.
getColumnMaxima(Collection<T>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Computes the maximum values of each provided column variable.
getColumnMin(Object) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Computes the minimum value of the provided column variable.
getColumnMinima(Collection<T>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Computes the minimum values of each provided column variable.
getColumnVariables() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the set of all column variables in the program matrix.
getCommentChars() - Method in class sbrt.shell.io.TextInputFile
Returns the commment characters used in this file.
getCommonElements(Collection<? extends E>, Collection<? extends E>) - Static method in class sbrt.kernel.utilities.Util
Returns a list of elements common to both provided collections.
getComputer(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.ExtremeCurrentManager
Returns an extreme current computer created from the provided input.
getComputer(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.ReverseRxnFluxIntervalManager
Returns the flux interval computer specified by the provided input.
getConditions() - Method in class sbrt.kernel.utilities.LogicalRelation
Returns the set of conditions of this logical relationship.
getConflicts() - Method in exception sbrt.kernel.io.ConflictingInputException
Returns the list of conflicting inputs.
getConstant() - Method in class sbrt.kernel.math.AbstractPolynomial
Returns the constant of this polynomial.
getConstant() - Method in interface sbrt.kernel.math.MathExpr
Returns the numerical constant of this mathematical expression.
getConstant() - Method in interface sbrt.kernel.math.Polynomial
Returns the numerical constant of this polynomial.
getConstraint(String) - Method in class sbrt.kernel.fba.FluxConstraints
Returns the flux constraint for the provided reaction.
getConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.FluxConstraints
Returns the constraint of the provided mathematical expression of reaction names.
getConstraints() - Method in interface sbrt.kernel.fba.Fluxome
Returns the set of all constraints for fluxes and mathematical expressions of fluxes in this fluxome.
getConstraints() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns all constraints in this fluxome.
getConstraints() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns all constraints in this fluxome.
getConstraints(ManagerInput<String, String>, PrintWriter, Fluxome, double) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Opens the file denoted by FbaOptManager.CONSTRAINTS_FILE in the provided manager input and returns the set of flux constraints it contains.
getConstraints(String, Fluxome, double) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns the set of constraints contained in the file with the provided name.
getConstraints(ManagerInput<String, String>, PrintWriter, Fluxome, double) - Static method in class sbrt.shell.mng.fba.RandomFluxVectorManager
Opens the file denoted by FbaOptManager.CONSTRAINTS_FILE in the provided manager input and returns the set of flux constraints it contains.
getConstraints(String, Fluxome, double) - Static method in class sbrt.shell.mng.fba.RandomFluxVectorManager
Returns the set of constraints contained in the file with the provided name.
getConstraintTolerance() - Method in class sbrt.kernel.math.geom.comp.CdHarComp
Returns the constraint tolerance.
getConstraintTolerance(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaManager
Parses and returns the value for FbaManager.CONSTRAINT_TOLERANCE in the provided manager input.
getConstraintTolerance(ManagerInput<String, String>) - Static method in class sbrt.shell.mng.fba.FbaManager
Parses and returns the value for FbaManager.CONSTRAINT_TOLERANCE in the provided manager input.
getConstraintTolerance(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.geom.CdHarManager
Parses and returns the value for CdHarManager.CONSTRAINT_TOLERANCE in the provided manager input.
getCorrName() - Method in class sbrt.ext.R.stat.RCorrelator
Returns the name of the correlation statistic computed by this R correlator.
getCorrName() - Method in class sbrt.ext.R.stat.RKendall
Returns kendall.
getCorrName() - Method in class sbrt.ext.R.stat.RPearson
Returns pearson.
getCorrName() - Method in class sbrt.ext.R.stat.RSpearman
Returns spearman.
getCount() - Method in class sbrt.kernel.utilities.AbstractProgressMonitor
Returns the number of times of increment() has been called.
getCvInputFile(ManagerInput<String, String>, PrintWriter, Fluxome, double) - Static method in class sbrt.shell.mng.fba.IntervalVariationManager
Returns the constraint variation input with the name denoted by IntervalVariationManager.CV_FILE in the provided manager input.
getCvInputFile(String, Fluxome, double) - Static method in class sbrt.shell.mng.fba.IntervalVariationManager
Returns the constraint variation input file with the provided name.
getCycles(F) - Method in interface sbrt.kernel.fba.comp.CycleComputer
Returns the set of all steady state cycles contained in the provided fluxome.
getCycles(IrrevRxnFluxome) - Method in class sbrt.kernel.fba.comp.SlpCycleComputer
Returns the set of all steady state cycles contained in the provided fluxome.
getCycles(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.FluxCapManager
Opens the file denoted by FluxCapManager.CYCLE_FILE in the provided manager input and returns the list of cycles it contains.
getDataHeaders(ManagerInput<String, String>, Fluxome) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Parses and returns the value for AbstractProcessManager.DATA_HEADERS in the provided manager input.
getDataHeaders(String, Fluxome) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Parses the provided data header string and returns the corresponding set.
getDefault() - Static method in class sbrt.kernel.io.WarningHandlerFactory
Returns the default warning handler.
getDeletionFile(ManagerInput<String, String>, PrintWriter, CatalyzedFluxome) - Static method in class sbrt.shell.mng.fba.CatalystDeletionManager
Parses and returns the value for CatalystDeletionManager.CATALYST_DELETION_FILE in the provided manager input.
getDeletionFile(String, CatalyzedFluxome) - Static method in class sbrt.shell.mng.fba.CatalystDeletionManager
Returns the catalyst input file with the provided name.
getDelimiter() - Method in class sbrt.shell.text.AbstractLinkedHashSetFormat
Returns the delimiter used to separate elements when producing a formatted string.
getDelimiter() - Method in class sbrt.shell.text.AbstractListFormat
Returns the delimiter used to separate elements when producing a formatted string.
getDelimiter() - Method in class sbrt.shell.text.AbstractMapEntryFormat
Returns the delimiter used to separate the key from the value in a key-value pair.
getDiffs(Map<? extends V, Interval>, Map<? extends V, Interval>, double) - Method in class sbrt.kernel.math.IntervalComparer
Returns the set of differences between the provided interval vectors.
getDiffs(Map<? extends V, Double>, Map<? extends V, Double>, double) - Method in class sbrt.kernel.math.VectorComparer
Returns the set of differences between the provided numerical vectors.
getDimension() - Method in exception sbrt.kernel.math.geom.DimensionException
Returns the invalid dimension.
getDirection() - Method in exception sbrt.kernel.math.InfeasibleSolutionException
Returns the variable, or direction in hyperspace, in which infeasibility was first detected.
getDist(Number[], Number[]) - Method in class sbrt.kernel.math.geom.comp.EuclideanDist
Computes and returns the Euclidean distance between the provided arrays.
getDist(Collection<? extends Number>, Collection<? extends Number>) - Method in class sbrt.kernel.math.geom.comp.EuclideanDist
Computes and returns the Euclidean distance between the provided collections.
getDist(Map<?, ? extends Number>, Map<?, ? extends Number>) - Method in class sbrt.kernel.math.geom.comp.EuclideanDist
Computes and returns the Euclidean distance between the provided maps.
getDist(String, String) - Method in class sbrt.kernel.math.geom.comp.Hamming
Computes and returns the Hamming distance between the provided strings.
getDist(Object[], Object[]) - Method in class sbrt.kernel.math.geom.comp.Hamming
Computes and returns the Hamming distance between the provided arrays.
getDist(Collection<?>, Collection<?>) - Method in class sbrt.kernel.math.geom.comp.Hamming
Computes and returns the Hamming distance between the provided collections.
getDist(Map<?, ?>, Map<?, ?>) - Method in class sbrt.kernel.math.geom.comp.Hamming
Computes and returns the Hamming distance between the provided maps.
getDist(Number[], Number[]) - Method in class sbrt.kernel.math.geom.comp.Taxicab
Computes and returns the Taxicab distance between the provided arrays.
getDist(Collection<? extends Number>, Collection<? extends Number>) - Method in class sbrt.kernel.math.geom.comp.Taxicab
Computes and returns the Taxicab distance between the provided collections.
getDist(Map<?, ? extends Number>, Map<?, ? extends Number>) - Method in class sbrt.kernel.math.geom.comp.Taxicab
Computes and returns the Taxicab distance between the provided maps.
getDOM(String) - Static method in class sbrt.shell.io.XmlFileFactory
Returns a DOM object for the file with the specified name.
getDoubleFormat() - Method in class sbrt.shell.text.fba.FbaOptFileLineFormatV1
Returns the format used for doubles.
getDoubleFormat() - Method in class sbrt.shell.text.math.BoundedIntervalFormatV1
Returns the double format used for bounds.
getDoubleFormat() - Method in class sbrt.shell.text.math.IntervalFormatV1
Returns the double format used for bounds.
getDoubleFormat() - Method in class sbrt.shell.text.PercentFormatVersion1
Returns the DoubleFormat used to parse and format the numerical percentage values.
getDoubleTester() - Method in class sbrt.kernel.math.IntervalEquiv
Returns the double equivalence tester used by this interval equivalence tester.
getDuplicates(Collection<E>) - Static method in class sbrt.kernel.utilities.Util
Returns a list of duplicate elements contained in the provided collection.
getDuration() - Method in class sbrt.kernel.utilities.AbstractProgressMonitor
Returns the elapsed time between the calls of start() and stop().
getDuration() - Method in interface sbrt.kernel.utilities.ProgressMonitor
Returns the current duration of the process being monitored.
getEdges() - Method in class sbrt.kernel.math.graph_theory.DirectedGraph
Returns the set of all edges contained in this graph.
getEdges(String) - Static method in class sbrt.shell.mng.graph_theory.PathIdManager
Parses the file with the provided name, and returns the set of edges it contains.
getEdges(String, DirEdgeFormat<N>) - Static method in class sbrt.shell.mng.graph_theory.PathIdManager
Parses the file with the provided name, and returns the set of edges it contains.
getElement(Object, Object) - Method in interface sbrt.kernel.math.algebra.DoubleMatrix
Returns the element of this matrix at the provided row and column indices.
getElement(Object, Object) - Method in class sbrt.kernel.math.algebra.DoubleMatrixWrap
Returns the element of this matrix at the provided row and column indices.
getElement(Object, Object) - Method in class sbrt.kernel.math.algebra.HashMatrix
Returns the element of this matrix at the provided row and column indices.
getElement(Object, Object) - Method in interface sbrt.kernel.math.algebra.Matrix
Returns the element of this matrix at the provided row and column indices.
getElement() - Method in class sbrt.kernel.math.algebra.MatrixElement
Returns the value of this matrix element.
getElement(Object, Object) - Method in class sbrt.kernel.math.algebra.MatrixWrap
Returns the element of this matrix at the provided row and column indices.
getElement(Object, Object) - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Returns the element of this matrix at the provided row and column indices.
getElement(Object, Object) - Method in class sbrt.kernel.math.algebra.TreeMatrix
Returns the element of this matrix at the provided row and column indices.
getElementaryModes(InputFile<String>, List<String>) - Method in class sbrt.shell.proc.fba.MetatoolOutputReader
Returns the elementary mode matrix contained in the provided Metatool output file.
getElementFormat() - Method in interface sbrt.shell.text.CollectionFormat
Returns the format object used for the elements of this collection format.
getElementFormat() - Method in class sbrt.shell.text.math.MatrixElementFormatV1
Returns the format used for matrix elements.
getElementFormatter() - Method in class sbrt.shell.text.AbstractLinkedHashSetFormat
Returns the formatter for the elements of this LinkedHashSet format.
getElementFormatter() - Method in class sbrt.shell.text.AbstractListFormat
Returns the formatter for the elements of this LinkedHashSet format.
getElementFormatter() - Method in class sbrt.shell.text.BoolRelFormatV1
Returns the formatter for the elements of this set format.
getElementFormatter() - Method in interface sbrt.shell.text.LinkedHashSetFormat
Returns the formatter for the elements of this set format.
getElementFormatter() - Method in interface sbrt.shell.text.ListFormat
Returns the formatter for the elements of this list format.
getElementFormatter() - Method in class sbrt.shell.text.SimpleListFormat
Returns the formatter for the elements of this list format.
getElementFormatter() - Method in class sbrt.shell.text.SimpleSetFormat
Returns the formatter for the elements of this set format.
getElementParser() - Method in class sbrt.shell.text.AbstractLinkedHashSetFormat
Returns the parser for the elements of this set format.
getElementParser() - Method in class sbrt.shell.text.AbstractListFormat
Returns the parser for the elements of this set format.
getElementParser() - Method in class sbrt.shell.text.BoolRelFormatV1
Returns the parser for the elements of this set format.
getElementParser() - Method in interface sbrt.shell.text.LinkedHashSetFormat
Returns the parser for the elements of this set format.
getElementParser() - Method in interface sbrt.shell.text.ListFormat
Returns the parser for the elements of this list format.
getElementParser() - Method in class sbrt.shell.text.SimpleListFormat
Returns the parser for the elements of this list format.
getElementParser() - Method in class sbrt.shell.text.SimpleSetFormat
Returns the parser for the elements of this set format.
getEnzIrrev() - Method in class sbrt.shell.proc.fba.MetatoolInputReader.Results
Returns the reaction names that are listed in the -ENZIRREV section of the input file.
getEnzRev() - Method in class sbrt.shell.proc.fba.MetatoolInputReader.Results
Returns the reaction names that are listed in the -ENZREV section of the input file.
getEnzymeChecker() - Method in class sbrt.shell.text.fba.CatalystListFormatV1
Returns the catalyst name verifier.
getEnzymeChecker() - Method in class sbrt.shell.text.fba.CatalystSetFormatV1
Returns the catalyst name verifier.
getEquations(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.algebra.LinearSolverManager
Returns the set of linear equations contained in the file with the provided name.
getEquations(String, PrintWriter) - Static method in class sbrt.shell.mng.algebra.LinearSolverManager
Returns the set of linear equations contained in the file with the provided name.
getEquations(String) - Static method in class sbrt.shell.mng.algebra.LinearSolverManager
Returns the set of linear equations contained in the file with the provided name.
getEquivIrrevRxnIds(T, Map<T, IrrevRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns the keys in the provided map that correspond to reactions that are stoichiometrically equivalent to the reaction in the map with the specified map key.
getEquivIrrevRxnIds(Map<T, IrrevRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns a collection of sets of the names of stoichiometrically equivalent reactions contained in the provided map.
getEquivIrrevRxns(T, Map<T, IrrevRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns the reactions in the provided map that are stoichiometrically equivalent to the reaction in the map with the provided map key.
getEquivRevExchRxnIds(Map<T, RevExchRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns a collection of sets of the names of stoichiometrically equivalent reactions contained in the provided map.
getEquivRevRxnIds(T, Map<T, RevRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns the keys in the provided map that correspond to reactions that are stoichiometrically equivalent to the reaction in the map with the specified map key.
getEquivRevRxnIds(Map<T, RevRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns a collection of sets of the names of stoichiometrically equivalent reactions contained in the provided map.
getEquivRevRxns(T, Map<T, RevRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns the reactions in the provided map that are stoichiometrically equivalent to the reaction in the map with the provided map key.
getEquivRxns(Fluxome) - Static method in class sbrt.kernel.fba.comp.RedundRxnRemover
Returns the equivalent reactions contained in the provided fluxome.
getEquivRxns() - Method in class sbrt.kernel.fba.proc.NetworkInfoProcess.Results
Returns the equivalent reactions contained in the fluxome.
getEquivSinkRxnIds(Map<T, SinkRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns a collection of sets of the names of stoichiometrically equivalent reactions contained in the provided map.
getEquivSourceRxnIds(Map<T, SourceRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns a collection of sets of the names of stoichiometrically equivalent reactions contained in the provided map.
getErrorWriter() - Method in class sbrt.shell.gui.SbrtOutputPane
Returns the print writer used for writing error messages to this output pane.
getExchangeRxn(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the exchange reaction in this fluxome with the provided name.
getExchangeRxn(String) - Method in interface sbrt.kernel.fba.MixedFluxome
Returns the exchange reaction in this fluxome with the provided name.
getExchangeRxn(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the exchange reaction in this fluxome with the provided name.
getExchangeRxnNames() - Method in interface sbrt.kernel.fba.Fluxome
Returns the set of names of all exchange reactions contained in this fluxome.
getExchangeRxnNames() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the set of names of all exchange reactions in this fluxome.
getExchangeRxnNames() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the set of names of all exchange reactions in this fluxome.
getExchangeRxns() - Method in interface sbrt.kernel.fba.Fluxome
Returns all of the exchange reactions contained in this fluxome.
getExchangeRxns() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns all of the exchange reactions contained in this fluxome.
getExchangeRxns(Collection<String>) - Method in interface sbrt.kernel.fba.MixedFluxome
Returns the exchange reactions with the provided names.
getExchangeRxns() - Method in interface sbrt.kernel.fba.MixedFluxome
Returns all of the exchange reactions contained in this fluxome.
getExchangeRxns() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns all of the exchange reactions contained in this fluxome.
getExchangeRxns(Collection<String>) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the exchange reactions with the provided names.
getExpr(V) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Converts a column variable to a single-term linear combination.
getExpr(Collection<V>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Converts a collection of column variables to a linear combination.
getExprConstraints() - Method in class sbrt.kernel.fba.FluxConstraints
Returns the constraints for mathematical expressions of fluxes.
getExpressions(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.utilities.VariableParticipationManager
Opens the file denoted by VariableParticipationManager.EXPRESSION_FILE in the provided manager input and returns the list of mathematical expressions it contains.
getFbaOptFileLineFormat() - Method in class sbrt.shell.io.fba.CofoofSource
Returns the FBA optimization file line format used to write data strings to files produced by this source.
getFbaOptFileLineFormat() - Method in class sbrt.shell.io.fba.ColumnOrFbaOptOutputFile
Returns the FBA optimization file line format used to write data strings to this file.
getFbaOptFileLineFormat() - Method in interface sbrt.shell.io.fba.FbaOptOutputFile
Returns the FBA optimization output file line format.
getFbaOptFileLineFormat() - Method in class sbrt.shell.io.fba.RowOrFbaOptOutputFile
Returns the FBA optimization file line format used to write data strings to this file.
getFbaOptFileLineFormat() - Method in class sbrt.shell.io.fba.SerFbaOptOutputFile
Returns the FBA optimization file line format used to supply a header object for objective values.
getFileFormat() - Method in class sbrt.shell.io.ComiFileSource
Returns the format used to create files of type ComiFile.
getFileFormat() - Method in class sbrt.shell.io.ComoFileSource
Returns the format used to create files of type ComoFile.
getFileFormat() - Method in class sbrt.shell.io.fba.CofoofSource
Returns the file format used to create files of type ColumnOrFbaOptOutputFile.
getFileFormat() - Method in class sbrt.shell.io.fba.RofoofSource
Returns the file format used to create files of type RowOrFbaOptOutputFile.
getFileFormat() - Method in class sbrt.shell.io.fba.SfoofSource
Returns the file format used to create files of type SerFbaOptOutputFile.
getFileFormat() - Method in class sbrt.shell.io.RomiFileSource
Returns the format used to create files of type RomiFile.
getFileFormat() - Method in class sbrt.shell.io.RomoFileSource
Returns the format used to create files of type RomoFile.
getFileFormat() - Method in class sbrt.shell.io.SerializedInputFile
Returns the format of this file.
getFileFormat() - Method in class sbrt.shell.io.SerializedOutputFile
Returns the format of this file.
getFileFormat() - Method in class sbrt.shell.io.SmoFileSource
Returns the format used to create files of type SmoFile.
getFileFormat() - Method in class sbrt.shell.io.TextInputFile
Returns the format of this file.
getFileFormat(ManagerInput<String, String>) - Static method in class sbrt.shell.mng.AbstractProcessManager
Returns the parsed value for AbstractProcessManager.FILE_FORMAT in the provided input.
getFileFormat(String) - Static method in class sbrt.shell.mng.AbstractProcessManager
Parses and returns the file format corresponding to the provided string.
getFileNameSource(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.AbstractProcessManager
Returns the parsed value for AbstractProcessManager.OUTPUT_FILE_NAME_FILE in the provided input and prints a descriptive message to the provided print writer.
getFilterKeys() - Method in class sbrt.shell.io.AbstractMapOutputFile
Returns the set of keys whose values will be written to this output file when a map is added.
getFilterKeys() - Method in class sbrt.shell.io.fba.SerFbaOptOutputFile
Returns the set of keys whose values will be written to this output file when results are added.
getFilterKeys() - Method in interface sbrt.shell.io.MapOutputFile
Returns the set of keys whose values will be written to this output file when a map is added.
getFilterKeys() - Method in class sbrt.shell.io.SmoFile
Returns the set of keys whose values will be written to this output file when a map is added.
getFluxBounds(Node) - Method in class sbrt.shell.text.fba.BiggRxnNodeParser
Returns the flux bounds of the provided reaction node.
getFluxBounds(Node) - Method in class sbrt.shell.text.fba.PalssonRxnNodeParser
Returns the flux bounds of the provided reaction node.
getFluxCap() - Method in exception sbrt.kernel.fba.comp.FluxCapException
Returns the invalid flux cap.
getFluxCaps() - Method in class sbrt.kernel.fba.comp.FluxCapComputer
Computes and returns all flux caps.
getFluxCaps() - Method in class sbrt.shell.io.fba.FluxCapInputFile
Returns the flux caps contained in this file.
getFluxCaps(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.MsFluxIntervalManager
Returns the flux caps contained in the file with the name specified by MsFluxIntervalManager.FLUX_CAP_FILE in the provided input.
getFluxConstraint(String) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Returns the current flux constraint on the reaction with the provided name.
getFluxConstraint(String) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Returns the current flux constraint on the reaction with the provided name.
getFluxConstraint(String) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the current flux constraint on the reaction with the provided name.
getFluxConstraint(String) - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Returns the current flux constraint for the reaction with the provided name.
getFluxConstraint(String) - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Returns the current flux constraint on the reaction with the provided name.
getFluxConstraint(String) - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Returns the flux constraint of the reaction with the provided name.
getFluxConstraint(String) - Method in interface sbrt.kernel.fba.Fluxome
Returns the flux constraint for the reaction with the provided name.
getFluxConstraint(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the flux constraint for the provided reaction.
getFluxConstraint(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the flux constraint for the provided reaction.
getFluxConstraints() - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Returns all current flux constraints.
getFluxConstraints() - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Returns all current flux constraints.
getFluxConstraints() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns all current flux constraints for each reaction in the fluxome used by this optimization computer.
getFluxConstraints() - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Returns all current flux constraints.
getFluxConstraints() - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Returns all current flux constraints.
getFluxConstraints() - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Returns the set of all constraints on single fluxes.
getFluxConstraints() - Method in class sbrt.kernel.fba.FluxConstraints
Returns the flux constraints for single reactions.
getFluxConstraints() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the constraints on each flux in this fluxome.
getFluxConstraints() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the constraints on each flux in this fluxome.
getFluxIntervalFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.FluxPlasticityManager
Returns the flux interval input with the name denoted by FluxPlasticityManager.FLUX_INTERVAL_FILE in the provided manager input.
getFluxIntervalFile(String, Fluxome) - Static method in class sbrt.shell.mng.fba.FluxPlasticityManager
Returns the flux interval input file with the provided name.
getFluxMax(String) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Computes the maximum flux of the reaction with the provided name.
getFluxMaxima(Collection<String>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Computes the maximum flux of each reaction with the provided names.
getFluxMaxima(Collection<String>, MutableProgressMonitor) - Method in class sbrt.kernel.fba.comp.ReverseRxnIntervalComp
Computes and returns the maximum fluxes of the reactions with the provided names.
getFluxMin(String) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Computes the minimum flux of the reaction with the provided name.
getFluxMinima(Collection<String>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Computes the minimum flux of each reaction with the provided names.
getFluxMinima(Collection<String>, MutableProgressMonitor) - Method in class sbrt.kernel.fba.comp.ReverseRxnIntervalComp
Computes and returns the minimum fluxes of the reactions with the provided names.
getFluxome() - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Returns the fluxome for which values will be computed.
getFluxome() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the fluxome used by this optimization computer.
getFluxome() - Method in class sbrt.kernel.fba.comp.FluxCapComputer
Returns the fluxome for which flux caps are computed.
getFluxome() - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Returns the fluxome that this flux constraint-variation computer uses.
getFluxome() - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Returns the fluxome used by this computer.
getFluxome() - Method in class sbrt.kernel.fba.proc.CatalystDeletionProcess
Returns the fluxome used by the reaction deletion computer.
getFluxome() - Method in class sbrt.kernel.fba.proc.CdHarFluxVectorProcess
Returns the fluxome for which flux vectors are to be generated.
getFluxome() - Method in class sbrt.kernel.fba.proc.CvCatalystDeletionProcess
Returns the fluxome used by the reaction deletion computer.
getFluxome() - Method in class sbrt.kernel.fba.proc.CvFbaOptProcess
Returns the fluxome used in this process.
getFluxome() - Method in class sbrt.kernel.fba.proc.CvFluxIntervalProcess
Returns the fluxome used in this process.
getFluxome() - Method in class sbrt.kernel.fba.proc.CvObjectiveFunctionProcess
Returns the fluxome used in this process.
getFluxome() - Method in class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Returns the fluxome used by the reaction deletion computer.
getFluxome() - Method in class sbrt.kernel.fba.proc.CycleIdProcess
Returns the fluxome used in this process.
getFluxome() - Method in class sbrt.kernel.fba.proc.ExtremeCurrentProcess
Returns the fluxome used in this process.
getFluxome() - Method in class sbrt.kernel.fba.proc.FbaOptProcess
Returns the fluxome used in this process.
getFluxome() - Method in class sbrt.kernel.fba.proc.FbaProcess
Returns the fluxome used in this process.
getFluxome() - Method in class sbrt.kernel.fba.proc.FbaSolverProcess
Returns the fluxome for which Sv = 0 is solved.
getFluxome() - Method in class sbrt.kernel.fba.proc.FluxActivityProcess
Returns the fluxome used in this flux activity process.
getFluxome() - Method in class sbrt.kernel.fba.proc.FluxCapProcess
Returns the fluxome for which flux caps are computed.
getFluxome() - Method in class sbrt.kernel.fba.proc.FluxIntervalProcess
Returns the fluxome used in this proces.
getFluxome() - Method in class sbrt.kernel.fba.proc.FluxomeReducerProcess
Returns the fluxome used in this process.
getFluxome() - Method in class sbrt.kernel.fba.proc.FluxPlasticityProcess
Returns the fluxome used in this flux plasticity process.
getFluxome() - Method in class sbrt.kernel.fba.proc.InitialPointGenerator
Returns the fluxome used in this initial point process.
getFluxome() - Method in class sbrt.kernel.fba.proc.NetworkInfoProcess
Returns the fluxome for which information is to be gathered.
getFluxome() - Method in class sbrt.kernel.fba.proc.ObjFunAnalysis
Returns the fluxome used in this process.
getFluxome() - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Returns the fluxome for which random constraints are to be generated.
getFluxome() - Method in class sbrt.kernel.fba.proc.RandomObjectiveGenerator
Returns the fluxome for which random objective functions are to be generated.
getFluxome() - Method in class sbrt.kernel.fba.proc.RedundRxnRemoverProcess
Returns the fluxome for which redundant reactions are to be removed.
getFluxome() - Method in class sbrt.kernel.fba.proc.RxnDeletionProcess
Returns the fluxome used by the reaction deletion computer.
getFluxome() - Method in class sbrt.kernel.fba.proc.SvCdHarFluxVectorProcess
Returns the fluxome for which flux vectors are to be generated.
getFluxome() - Method in class sbrt.kernel.fba.proc.SvInitialPointProcess
Returns the fluxome used in this initial point process.
getFluxome() - Method in class sbrt.shell.io.fba.FluxCapInputFile
Returns the fluxome used to verify reaction names.
getFluxome() - Method in interface sbrt.shell.text.fba.CatalystListFormat
Returns the fluxome used to verify catalyst names.
getFluxome() - Method in class sbrt.shell.text.fba.CatalystListFormatV1
Returns the fluxome used to verify catalyst names.
getFluxome() - Method in interface sbrt.shell.text.fba.CatalystSetFormat
Returns the fluxome used to verify enzyme names.
getFluxome() - Method in class sbrt.shell.text.fba.CatalystSetFormatV1
Returns the fluxome used to verify catalyst names.
getFluxome() - Method in class sbrt.shell.text.fba.CatalystVerifier
Returns the fluxome used to create this catalyst name verifier.
getFluxome() - Method in class sbrt.shell.text.fba.ChemSpeciesVerifier
Returns the fluxome used to create this chemical species verifier.
getFluxome() - Method in interface sbrt.shell.text.fba.ConstraintsFileLineFormat
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.ConstraintsFileLineFormatV1
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.ConstraintsFileLineFormatV2
Returns the fluxome used to verify reaction names.
getFluxome() - Method in interface sbrt.shell.text.fba.FbaOptFileLineFormat
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.FbaOptFileLineFormatV1
Returns the fluxome used to verify reaction names.
getFluxome() - Method in interface sbrt.shell.text.fba.FbaOptHeaderFormatter
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.FbaOptHeaderFormatterV1
Returns the fluxome used to verify reaction names.
getFluxome() - Method in interface sbrt.shell.text.fba.FbaOptHeaderParser
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.FbaOptHeaderParserV1
Returns the fluxome used to verify reaction names.
getFluxome() - Method in interface sbrt.shell.text.fba.FluxCapFormat
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.FluxCapFormatV1
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.FluxomeSolFileLineFormatV1
Returns the fluxome used to verify reaction names.
getFluxome() - Method in interface sbrt.shell.text.fba.FluxomeSolutionFileLineFormat
Returns the fluxome used to verify reaction names.
getFluxome() - Method in interface sbrt.shell.text.fba.FluxVectorFormat
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.FluxVectorFormatV1
Returns the fluxome used to verify reaction names.
getFluxome() - Method in interface sbrt.shell.text.fba.RxnNameExprFormat
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.RxnNameExprFormatV1
Returns the fluxome used to verify reaction names.
getFluxome() - Method in interface sbrt.shell.text.fba.RxnNameListFormat
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.RxnNameListFormatV1
Returns the fluxome used to verify reaction names.
getFluxome() - Method in interface sbrt.shell.text.fba.RxnNameOrExprFormat
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.RxnNameOrExprFormatV1
Returns the fluxome used to verify reaction names.
getFluxome() - Method in interface sbrt.shell.text.fba.RxnNameSetFormat
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.RxnNameSetFormatV1
Returns the fluxome used to verify reaction names.
getFluxome() - Method in class sbrt.shell.text.fba.RxnNameVerifier
Returns the fluxome used to create this reaction name checker.
getFluxomeSolution(ManagerInput<String, String>, PrintWriter, Fluxome, double) - Static method in class sbrt.shell.mng.fba.FbaManager
Opens the file denoted by FbaManager.SYSTEM_SOLUTION_FILE in the provided manager input and returns the linear system solution it contains.
getFluxValue(Node) - Method in class sbrt.shell.text.fba.BiggRxnNodeParser
Returns the flux value of the provided reaction node.
getFluxValue(Node) - Method in class sbrt.shell.text.fba.PalssonRxnNodeParser
Returns the flux value of the provided reaction node.
getFluxVector() - Method in class sbrt.kernel.fba.comp.CdHarFluxComp.Results
Returns the random interior flux vector that was computed.
getFluxVector() - Method in class sbrt.kernel.fba.comp.FbaOptimizer.Results
Returns the flux vector computed during optimization.
getFluxVector() - Method in class sbrt.kernel.fba.comp.InitialPointComputer.Results
Returns the computed flux vector.
getFluxVector() - Method in exception sbrt.kernel.fba.comp.InvalidFluxVectorException
Returns the invalid flux vector;
getFluxVector(ManagerInput<String, String>, PrintWriter, Fluxome, double) - Static method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Opens the file denoted by CdHarManager.INITIAL_POINT_FILE in the provided manager input and returns the flux vector it contains.
getFluxVector(ManagerInput<String, String>, PrintWriter, Fluxome, double) - Static method in class sbrt.shell.mng.fba.RandomFluxVectorManager
Opens the file denoted by FbaManager.FLUX_VECTOR_FILE in the provided manager input and returns the flux vector it contains.
getFluxVector(String, Fluxome, double) - Static method in class sbrt.shell.mng.fba.RandomFluxVectorManager
Returns the flux vector contained in the file with the provided name.
getFluxVectorFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.FluxActivityManager
Returns the flux vector input file specified by the provided input.
getFluxVectorFile(String, FileFormat, Fluxome) - Static method in class sbrt.shell.mng.fba.FluxActivityManager
Returns the flux vector input file with the provided name.
getFluxVectorFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.InitialPointManager
Returns an empty output file that is suitable for storing a single flux vector.
getFreeVariables() - Method in class sbrt.kernel.math.algebra.HashLinearSystemSolution
Returns the set of free variables contained in this solution.
getFreeVariables() - Method in interface sbrt.kernel.math.algebra.LinearSystemSolution
Returns the set of free variables contained in this solution.
getGenes(Node) - Method in class sbrt.shell.text.fba.BiggRxnNodeParser
Calls BiggRxnNodeParser.getCatalysts(Node, String) with "GENE ASSOCIATION:" as the prefix.
getGenes(Node) - Method in class sbrt.shell.text.fba.PalssonRxnNodeParser
Calls PalssonRxnNodeParser.getCatalysts(Node, String) with "GENE_ASSOCIATION:" as the prefix.
getGraph() - Method in class sbrt.kernel.math.graph_theory.comp.PathFinder
Returns the graph in which pathways will be computed.
getGraph(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.graph_theory.PathIdManager
Opens the file denoted by PathIdManager.EDGE_FILE in the provided manager input and returns the directed graph it contains.
getGraph(String) - Static method in class sbrt.shell.mng.graph_theory.PathIdManager
Parses the file with the provided name, and returns the directed graph it contains.
getGraph(String, DirEdgeFormat<N>) - Static method in class sbrt.shell.mng.graph_theory.PathIdManager
Parses the file with the provided name, and returns the directed graph it contains.
getInactive() - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Returns the constraint used for inactive reactions.
getInactive(ManagerInput<String, String>) - Static method in class sbrt.shell.mng.fba.RandomConstraintsManager
Parses and returns the value for RandomConstraintsManager.INACTIVE in the provided manager input.
getIndexFormat() - Method in class sbrt.shell.text.math.MatrixElementFormatV1
Returns the format used for matrix elements.
getIndices() - Method in class sbrt.kernel.math.algebra.MatrixElement
Returns the pair of indices.
getInitialPoint(ManagerInput<String, String>, PrintWriter, Set<String>) - Static method in class sbrt.shell.mng.geom.CdHarManager
Opens the file with the name denoted by CdHarManager.INITIAL_POINT_FILE and return the vector it contains.
getInitialPoint(String, PrintWriter, Set<String>) - Static method in class sbrt.shell.mng.geom.CdHarManager
Opens the file with the provided name and return the vector it contains.
getInitialPoint(String, Set<String>) - Static method in class sbrt.shell.mng.geom.CdHarManager
Opens the file with the provided name and return the vector it contains.
getInitialPoint(String, MapFormat<String, Double>, Set<String>) - Static method in class sbrt.shell.mng.geom.CdHarManager
Opens the file with the provided name and return the vector it contains.
getInputFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.ObjectiveFunctionManager
Returns the file denoted by ObjectiveFunctionManager.OBJ_FUNCT_FILE in the provided manager input.
getInputFile(String, FileFormat, Fluxome) - Static method in class sbrt.shell.mng.fba.ObjectiveFunctionManager
Returns the input file with the provided name.
getInputFile(String, Fluxome) - Static method in class sbrt.shell.mng.fba.ObjectiveFunctionManager
Returns the input file with the provided name.
getInputFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.RxnDeletionManager
Parses and returns the value for RxnDeletionManager.RXN_DELETION_FILE in the provided manager input.
getInputFile(String, Fluxome) - Static method in class sbrt.shell.mng.fba.RxnDeletionManager
Returns the reaction name input file with the provided name.
getInputIrrevRxnFormat() - Method in class sbrt.shell.proc.fba.SimpleRxnFileReader
Returns the parser used for irreversible reactions in the provided input file.
getInputRevRxnFormat() - Method in class sbrt.shell.proc.fba.SimpleRxnFileReader
Returns the parser used for reversible reactions in the provided input file.
getInternalRxn(String) - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the internal reaction in this fluxome with the provided name.
getInternalRxn(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the internal reaction in this fluxome with the provided name.
getInternalRxn(String) - Method in interface sbrt.kernel.fba.MixedFluxome
Returns the internal reaction in this fluxome with the provided name.
getInternalRxn(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the internal reaction in this fluxome with the provided name.
getInternalRxnNames() - Method in interface sbrt.kernel.fba.Fluxome
Returns the set of names of all internal chemical reactions contained in this fluxome.
getInternalRxnNames() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the set of names of all internal reactions in this fluxome.
getInternalRxnNames() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the set of names of all internal reactions in this fluxome.
getInternalRxns() - Method in interface sbrt.kernel.fba.Fluxome
Returns the set of all internal chemical reactions contained in this fluxome.
getInternalRxns() - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns all of the internal reactions in this fluxome.
getInternalRxns(Collection<String>) - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the internal reactions with the provided names.
getInternalRxns() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns all of the internal reactions in this fluxome.
getInternalRxns(Collection<String>) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the internal reactions whose names appear in the provided collection of reaction names.
getInternalRxns() - Method in interface sbrt.kernel.fba.MixedFluxome
Returns all of the internal reactions in this fluxome.
getInternalRxns(Collection<String>) - Method in interface sbrt.kernel.fba.MixedFluxome
Returns the internal reactions with the provided names.
getInternalRxns() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns all of the internal reactions in this fluxome.
getInternalRxns(Collection<String>) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the internal reactions whose names appear in the provided collection of reaction names.
getInterval(String, Interval, double, double) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Returns the provided minimum and maximum fluxes as an interval.
getInterval1() - Method in class sbrt.kernel.math.IntervalComparer.Diff
Returns the "first" interval of the pair of intervals.
getInterval2() - Method in class sbrt.kernel.math.IntervalComparer.Diff
Returns the "second" interval of the pair of intervals.
getIntervalFormat() - Method in class sbrt.shell.text.math.BoundedIntervalFormatV1
Returns the interval format used by this format.
getIntervalInputFile(String, Fluxome, MapFormat<LinearComb<String>, Interval>, double) - Static method in class sbrt.shell.mng.fba.IntervalVariationManager
Returns the flux interval input file with the provided name.
getIntervalInputFile(String, Fluxome, double) - Static method in class sbrt.shell.mng.fba.IntervalVariationManager
Returns the flux interval input file with the provided name.
getIntervals(Map<String, Double>, Map<String, Double>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Returns the provided minima and maxima as intervals.
getIntervals() - Method in interface sbrt.kernel.fba.comp.FluxIntervalComputer
Computes and returns the intervals of every flux in the fluxome used by this flux interval computer.
getIntervals(Collection<String>) - Method in interface sbrt.kernel.fba.comp.FluxIntervalComputer
Computes and returns the flux intervals of the reactions with the provided names.
getIntervals() - Method in class sbrt.kernel.fba.comp.MsFluxIntervalComputer
Computes and returns the intervals of every flux in the fluxome used to construct this flux interval computer.
getIntervals(Collection<String>) - Method in class sbrt.kernel.fba.comp.MsFluxIntervalComputer
Computes and returns the flux intervals of the reactions with the provided names.
getIntervals() - Method in class sbrt.kernel.fba.comp.ReverseRxnIntervalComp
Computes and returns the intervals of every flux in the fluxome used to construct this flux interval computer.
getIntervals(Collection<String>) - Method in class sbrt.kernel.fba.comp.ReverseRxnIntervalComp
Computes and returns the flux intervals of the reactions with the provided names.
getIntervals() - Method in class sbrt.kernel.fba.comp.SimpleFluxIntervalComputer
Computes and returns the intervals of every flux in the fluxome used to construct this flux interval computer.
getIntervals(Collection<String>) - Method in class sbrt.kernel.fba.comp.SimpleFluxIntervalComputer
Computes and returns the flux intervals of the reactions with the provided names.
getIntervals(ManagerInput<String, String>, PrintWriter, Fluxome, double) - Static method in class sbrt.shell.mng.fba.InitialPointManager
Opens the file denoted by InitialPointManager.FLUX_INTERVAL_FILE in the provided manager input and returns the set of flux intervals it contains.
getIntervals(String, Fluxome, double) - Static method in class sbrt.shell.mng.fba.InitialPointManager
Returns the set of flux intervals contained in the file with the provided name.
getIrrevComp(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.MsFluxIntervalManager
Returns the flux interval computer specified by the provided input.
getIrrevConstraint() - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Returns the constraint used for active irreversible reactions.
getIrrevConstraint(ManagerInput<String, String>) - Static method in class sbrt.shell.mng.fba.RandomConstraintsManager
Parses and returns the value for RandomConstraintsManager.IRREV_CONSTRAINT in the provided manager input.
getIrrevRxnComp(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Creates and returns an FBA optimization computer based on the provided input.
getIrrevRxnFluxome(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaManager
Opens the file denoted by FbaManager.RXN_FILE in the provided manager input and returns the fluxome it contains.
getIrrevRxnFluxome(String, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns the fluxome contained in the file with the provided name.
getIrrevRxnFluxome(String) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns the fluxome contained in the file with the provided name.
getIrrevRxnFluxome(String, String) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns the fluxome contained in the files with the provided names.
getIrrevRxnFluxome(String, String, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns the fluxome contained in the files with the provided names.
getIrrevRxnFluxome(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Creates and returns a fluxome based on the provided input.
getIrrevRxnFluxome(ManagerInput<String, String>, PrintWriter, double) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Creates and returns a fluxome based on the provided input.
getIrrevRxnFluxome(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.RandomFluxVectorManager
Creates and returns a fluxome based on the provided input.
getIrrevRxnFormat() - Method in class sbrt.shell.text.fba.RxnFormatV1
Returns the format used for irreversible reactions.
getIterations() - Method in class sbrt.kernel.fba.proc.CdHarFluxVectorProcess
Returns the total number of flux vectors to be generated.
getIterations() - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Returns the number of sets of random constraints to be generated.
getIterations(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.AbstractProcessManager
Returns the parsed value for AbstractProcessManager.ITERATIONS in the provided input and prints a descriptive message to the provided print writer.
getKeyFormat() - Method in class sbrt.shell.text.ColonMapEntryFormatV1
Returns the format used for keys.
getKeyFormat() - Method in class sbrt.shell.text.EqualsMapEntryFormatV1
Returns the format used for keys.
getKeyFormatter() - Method in class sbrt.shell.text.AbstractMapFormat
Returns the formatter used for keys.
getKeyParser() - Method in class sbrt.shell.text.AbstractMapFormat
Returns the parser used for keys.
getKeys() - Method in class sbrt.shell.io.ComiFile
Returns the map keys (column headers) contained in this file.
getKeys() - Method in class sbrt.shell.io.RomiFile
Returns the keys of the map contained in this file.
getLargest(double, double) - Static method in class sbrt.kernel.utilities.Util
Returns the largest of the provided numbers.
getLargest(int, int) - Static method in class sbrt.kernel.utilities.Util
Returns the largest of the provided numbers.
getLeftPadding() - Method in class sbrt.shell.text.AbstractMapEntryFormat
Returns the left padding used to create formatted string representations of key-value pairs.
getLinearCombFormat() - Method in class sbrt.shell.text.chem.IrrevRxnFormatV1
Returns the format used for stoichiometric expressions.
getLinearCombFormat() - Method in class sbrt.shell.text.chem.RevRxnFormatV1
Returns the format used for stoichiometric expressions.
getLinearCombFormat() - Method in class sbrt.shell.text.fba.IrrevRxnFormatV1
Returns the format used for stoichiometric expressions.
getLinearCombFormat() - Method in class sbrt.shell.text.fba.IrrevRxnFormatV2
Returns the format used for stoichiometric expressions.
getLinearCombFormat() - Method in class sbrt.shell.text.fba.RevRxnFormatV1
Returns the format used for stoichiometric expressions.
getLinearCombFormat() - Method in class sbrt.shell.text.fba.RevRxnFormatV2
Returns the format used for stoichiometric expressions.
getLinearCombFormat() - Method in class sbrt.shell.text.fba.RxnNameOrExprFormatV1
Returns the reaction name expression format.
getLineFormat() - Method in class sbrt.shell.io.ComiFileSource
Returns the map format used to create files of type ComiFile.
getLineFormat() - Method in class sbrt.shell.io.ComoFileSource
Returns the map format used to create files of type ComoFile.
getLineFormat() - Method in class sbrt.shell.io.RomiFileSource
Returns the map format used to create files of type RomiFile.
getLineFormat() - Method in class sbrt.shell.io.RomoFileSource
Returns the map format used to create files of type RomoFile.
getLineFormat() - Method in class sbrt.shell.io.TextInputFile
Returns the format used to parse lines of this file.
getLineFormat() - Method in class sbrt.shell.io.TextOutputFile
Returns the format used to write lines to this file.
getLineFormat() - Method in class sbrt.shell.proc.fba.SimpleRxnFileReader
Returns the format used for individual lines in the input and output files.
getLinerCombFormat() - Method in class sbrt.shell.text.fba.RxnNameExprFormatV1
Returns the format used for linear combination.
getList() - Static method in class sbrt.shell.text.SpecialChars
Returns a list of the characters contained in this class.
getListFormat() - Method in class sbrt.shell.text.AbstractMapFormat
Returns the format used for lists of values.
getListFormat() - Method in class sbrt.shell.text.AppInputFileLineFormatVersion1
Returns the format used for lists of values.
getListFormat() - Method in class sbrt.shell.text.ColonMapFormatV1
Returns the format used for lists of values.
getListFormat() - Method in class sbrt.shell.text.EqualsMapFormatV1
Returns the format used for lists of values.
getListFormat() - Method in class sbrt.shell.text.fba.CatalystListFormatV1
Returns the format used for lists of catalyst names.
getListFormat() - Method in class sbrt.shell.text.fba.ConstraintsFileLineFormatV1
Returns the format used for lists of values.
getListFormat() - Method in class sbrt.shell.text.fba.ConstraintsFileLineFormatV2
Returns the format used for lists of values.
getListFormat() - Method in class sbrt.shell.text.fba.FluxCapFormatV1
Returns the format used for lists of values.
getListFormat() - Method in class sbrt.shell.text.fba.FluxomeSolFileLineFormatV1
Returns the format used for lists of values.
getListFormat() - Method in class sbrt.shell.text.fba.FluxVectorFormatV1
Returns the format used for lists of values.
getListFormat() - Method in class sbrt.shell.text.fba.IrfFormatV1
Returns the format used for lists of reactions.
getListFormat() - Method in class sbrt.shell.text.fba.MixedFluxomeFormatV1
Returns the format used for lists of reactions.
getListFormat() - Method in class sbrt.shell.text.fba.RxnNameListFormatV1
Returns the format used for lists of reaction names.
getListFormat() - Method in class sbrt.shell.text.SimpleListFormat
Returns the underlying list format.
getLower() - Method in exception sbrt.kernel.math.IllegalBoundsException
Returns the lower bound used to create this exception.
getLower() - Method in class sbrt.kernel.math.Interval
Returns the lower bound (or endpoint) of this interval.
getLowerBound(Node) - Method in class sbrt.shell.text.fba.BiggRxnNodeParser
Returns the lower flux bound of the provided reaction node.
getLowerBound(Node) - Method in class sbrt.shell.text.fba.PalssonRxnNodeParser
Returns the lower flux bound of the provided reaction node.
getMap() - Method in class sbrt.shell.io.RomiFile
Returns the map contained in this file.
getMapEntryFormat() - Method in class sbrt.shell.text.AbstractMapFormat
Returns the format used for variable-value pairs.
getMapEntryFormat() - Method in class sbrt.shell.text.AppInputFileLineFormatVersion1
Returns the format used for variable-value pairs.
getMapEntryFormat() - Method in class sbrt.shell.text.ColonMapFormatV1
Returns the format used for variable-value pairs.
getMapEntryFormat() - Method in class sbrt.shell.text.EqualsMapFormatV1
Returns the format used for variable-value pairs.
getMapEntryFormat() - Method in class sbrt.shell.text.fba.ConstraintsFileLineFormatV1
Returns the format used for variable-value pairs.
getMapEntryFormat() - Method in class sbrt.shell.text.fba.ConstraintsFileLineFormatV2
Returns the format used for variable-value pairs.
getMapEntryFormat() - Method in class sbrt.shell.text.fba.FluxCapFormatV1
Returns the format used for variable-value pairs.
getMapEntryFormat() - Method in class sbrt.shell.text.fba.FluxomeSolFileLineFormatV1
Returns the format used for variable-value pairs.
getMapEntryFormat() - Method in class sbrt.shell.text.fba.FluxVectorFormatV1
Returns the format used for variable-value pairs.
getMapEntryFormat() - Method in class sbrt.shell.text.fba.IrfFormatV1
Returns the format used for reaction name-reaction pairs.
getMapEntryFormat() - Method in class sbrt.shell.text.fba.MixedFluxomeFormatV1
Returns the format used for reaction name-reaction pairs.
getMapFormat() - Method in class sbrt.shell.io.AbstractMapInputFile
Returns the map format used to parse this file.
getMapFormat() - Method in class sbrt.shell.io.AbstractMapOutputFile
Returns the format used to write lines to this file.
getMapFormat() - Method in class sbrt.shell.io.fba.FluxCapInputFile
Returns the map format used to parse this file.
getMapFormat() - Method in interface sbrt.shell.io.MapTextFile
Returns the map format used by this file.
getMatrix(IrrevRxnFluxome) - Method in interface sbrt.kernel.fba.comp.ExtremeCurrentComputer
Returns the extreme current matrix for the provided fluxome.
getMatrix(IrrevRxnFluxome, MutableProgressMonitor) - Method in interface sbrt.kernel.fba.comp.ExtremeCurrentComputer
Returns the extreme current matrix for the provided fluxome.
getMatrix(IrrevRxnFluxome) - Method in class sbrt.kernel.fba.comp.SlpExCurrComputerV2
Returns the extreme current matrix for the provided fluxome.
getMatrix(IrrevRxnFluxome, MutableProgressMonitor) - Method in class sbrt.kernel.fba.comp.SlpExCurrComputerV2
Returns the extreme current matrix for the provided fluxome.
getMatrix(ComiFile<String, Double>) - Static method in class sbrt.shell.io.ComiFile
Reads the provided column-oriented map input file and returns its contents as a sparse matrix.
getMax(MathExpr<?>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the results of computing the maximum value of the provided objective function.
getMaxima(Collection<E>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Computes the maximum value of each provided objective function.
getMaximum(String) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Computes the maximum flux of the reaction with the provided name.
getMaximum(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Computes the maximum value of the provided objective function.
getMaximum(MathExpr<?>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Computes the maximum value of the provided objective function.
getMaximumFluxes(Collection<String>, MutableProgressMonitor) - Method in class sbrt.kernel.fba.comp.SimpleFluxIntervalComputer
Computes and returns the maximum fluxes of the reactions with the provided names.
getMaxObstructedMoves(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.geom.CdHarManager
Parses and returns the value for CdHarManager.MAX_OBSTRUCTED_MOVES in the provided manager input.
getMaxWastedMoves() - Method in class sbrt.kernel.fba.proc.CdHarFluxVectorProcess
Returns the allowed number of wasted moves.
getMaxWithRxnsMinimized(String, Set<String>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Computes the maximum flux of the reaction with the provided name while constraining the fluxes of the provided reactions to their minimum.
getMean() - Method in class sbrt.kernel.math.stat.NormalDist
Returns the mean, or average, of this distribution.
getMessage() - Method in exception sbrt.shell.ApplicationException
Returns the error message of this process exception.
getMetExt() - Method in class sbrt.shell.proc.fba.MetatoolInputReader.Results
Returns the chemical species that are listed in the -METEXT section of the input file.
getMetInt() - Method in class sbrt.shell.proc.fba.MetatoolInputReader.Results
Returns the chemical species that are listed in the -METINT section of the input file.
getMin(MathExpr<?>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the results of computing the minimum value of the provided objective function.
getMinChordLength() - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Returns the minimum length a computed chord must have to be considered successful.
getMinChordLength() - Method in class sbrt.kernel.math.geom.comp.CdHarComp
Returns the minimum length a computed chord must have to be considered successful.
getMinChordLength(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.geom.CdHarManager
Parses and returns the value for CdHarManager.MIN_CHORD_LENGTH in the provided manager input.
getMinima(Collection<E>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Computes the minimum value of each provided objective function.
getMinimum(String) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Computes the minimum flux of the reaction with the provided name.
getMinimum(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Computes the minimum value of the provided objective function.
getMinimum(MathExpr<?>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Computes the minimum value of the provided objective function.
getMixedComp(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Creates and returns a coordinate-direction hit-and-run flux vector computer using the provided input.
getMixedComp(ManagerInput<String, String>, PrintWriter, MixedFluxome, double) - Static method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Creates and returns a coordinate-direction hit-and-run flux vector computer using the provided input.
getMixedComp(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Creates and returns an FBA optimization computer based on the provided input.
getMixedComp(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.InitialPointManager
Creates and returns an FBA optimization computer based on the provided input.
getMixedComp(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
Returns the flux interval computer specified by the provided input.
getMixedDelComp(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.RxnDeletionManager
Returns a reaction deletion computer created from the provided input.
getMixedFluxome(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaManager
Opens the file denoted by FbaManager.RXN_FILE in the provided manager input and returns the fluxome it contains.
getMixedFluxome(String, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns the fluxome contained in the file with the provided name.
getMixedFluxome(String) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns the fluxome contained in the file with the provided name.
getMixedFluxome(String, String) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns the fluxome contained in the files with the provided names.
getMixedFluxome(String, String, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns the fluxome contained in the files with the provided names.
getMixedFluxome(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Creates and returns a fluxome based on the provided input.
getMixedFluxome(ManagerInput<String, String>, PrintWriter, double) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Creates and returns a fluxome based on the provided input.
getMixedFluxome(ManagerInput<String, String>, PrintWriter, double) - Static method in class sbrt.shell.mng.fba.InitialPointManager
Creates and returns a fluxome based on the provided input.
getMultiColOrOutputFiles(ManagerInput<String, String>, PrintWriter, Iterator<String>, String, F) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns a source of column-oriented FBA optimization output files.
getMultiFileOutput(ManagerInput<String, String>, PrintWriter, Iterator<String>, String, F) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns a source of FBA optimization output files.
getMultiFluxVectorOutputFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Returns an empty output file that is suitable for storing multiple flux vectors.
getMultiFluxVectorOutputFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns an empty output file that is suitable for storing multiple flux vectors.
getMultiFluxVectorOutputFile(String, FileFormat, Set<String>, Fluxome) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns an empty output file that is suitable for storing multiple flux vectors.
getMultiResultsOutputFile(ManagerInput<String, String>, PrintWriter, F) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns an empty output file that is suitable for storing multiple FBA optimization results.
getMultiResultsOutputFile(String, FileFormat, Set<String>, F) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns an empty output file that is suitable for storing multiple FBA optimization results.
getMultiResultsOutputFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
Returns an empty output file that is suitable for storing multiple sets of flux interval results.
getMultiResultsOutputFile(String, Set<String>, Fluxome) - Static method in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
Returns an empty output file that is suitable for storing multiple sets of flux interval results.
getMultiRowOrOutputFiles(ManagerInput<String, String>, PrintWriter, Iterator<String>, F) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns a source of row-oriented FBA optimization output files.
getMultiSerOutputFiles(ManagerInput<String, String>, PrintWriter, Iterator<String>, String, F) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns a source of serialized FBA optimization output files.
getN() - Method in class sbrt.kernel.math.stat.comp.TauResult
Returns the sample size.
getN1() - Method in class sbrt.kernel.math.stat.comp.MannWhitneyResults
Returns the size of the larger sample.
getN1(int, int) - Method in class sbrt.kernel.math.stat.comp.MannWhitneyU
Returns the largest provided sample size.
getN2() - Method in class sbrt.kernel.math.stat.comp.MannWhitneyResults
Returns the size of the smaller sample.
getN2(int, int) - Method in class sbrt.kernel.math.stat.comp.MannWhitneyU
Returns the smallest provided sample size.
getName() - Method in class sbrt.kernel.io.AbstractResultsManager
Returns an empty string.
getName() - Method in interface sbrt.kernel.io.ResultsManager
Returns the name of this results manager.
getName() - Method in class sbrt.shell.io.AbstractMapOutputFile
Returns the canonical name of this file.
getName() - Method in class sbrt.shell.io.fba.ColumnOrFbaOptOutputFile
Returns the canonical name of this file.
getName() - Method in class sbrt.shell.io.fba.RowOrFbaOptOutputFile
Returns the canonical name of this file.
getName() - Method in class sbrt.shell.io.fba.SerFbaOptOutputFile
Returns the canonical name of this file.
getName() - Method in class sbrt.shell.io.FileFormat
Returns the name of this file format.
getName() - Method in class sbrt.shell.io.MultiOutputFiles
Returns the name of the current file.
getName() - Method in class sbrt.shell.io.ProcessInputFile
Returns the canonical name of this file.
getName() - Method in class sbrt.shell.io.SerializedOutputFile
Returns the canonical name of this file.
getName() - Method in class sbrt.shell.io.TextOutputFile
Returns the canonical name of this file.
getName() - Method in interface sbrt.shell.mng.ManagerInput
Returns the name of this manager input.
getName() - Method in class sbrt.shell.mng.MapManagerInput
Returns the name of this manager input.
getNeighbors(Object) - Method in class sbrt.kernel.math.graph_theory.DirectedGraph
Returns the neighboring nodes of the provided node.
getNeverActive(Map<String, Interval>, double) - Method in class sbrt.kernel.fba.analysis.FluxIntervalAnalyzer
Returns the never-active fluxes in the provided map.
getNeverActive() - Method in class sbrt.kernel.fba.proc.FluxPlasticityProcess.Results
Returns the set of fluxes that are never active.
getNodes() - Method in class sbrt.kernel.math.graph_theory.DirectedGraph
Returns the set of all nodes contained in this graph.
getNumActiveFluxes(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.RandomConstraintsManager
Parses and returns the value for RandomConstraintsManager.NUM_ACTIVE_FLUXES in the provided manager input.
getNumberFormat() - Method in class sbrt.shell.text.math.CoeffFormatV1
Returns the format used for numerical values.
getNumberFormat() - Method in class sbrt.shell.text.math.CoeffFormatV2
Returns the format used for numerical values.
getObjectiveFunction() - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Returns the current objective function.
getObjectiveFunction() - Method in class sbrt.kernel.fba.proc.CatalystDeletionProcess
Returns the current objective function.
getObjectiveFunction() - Method in class sbrt.kernel.fba.proc.CvCatalystDeletionProcess
Returns the current objective function.
getObjectiveFunction() - Method in class sbrt.kernel.fba.proc.CvFbaOptProcess
Returns the current objective function.
getObjectiveFunction() - Method in class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Returns the current objective function.
getObjectiveFunction() - Method in class sbrt.kernel.fba.proc.FbaOptProcess
Returns the current objective function.
getObjectiveFunction() - Method in class sbrt.kernel.fba.proc.RxnDeletionProcess
Returns the current objective function.
getObjectiveValue() - Method in class sbrt.ext.cplex.CplexSolver
Returns the most recently computed objective value.
getObjectiveValue() - Method in class sbrt.ext.glpk.GlpkSolver
Returns the most recently computed objective value.
getObjectiveValue() - Method in class sbrt.kernel.fba.comp.FbaOptimizer.Results
Returns the computed objective value.
getObjectiveValue() - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Returns the most recently computed objective value.
getObjFunc(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Parses and returns the value for FbaOptManager.OBJECTIVE_FUNCTION in the provided manager input.
getObjFunction() - Method in exception sbrt.kernel.fba.comp.FbaOptException
Returns the objective function whose optimal value could not be found.
getObjValueHeader() - Method in interface sbrt.shell.text.fba.FbaOptFileLineFormat
Returns the header used to indicate the value of the objective function.
getObjValueHeader() - Method in class sbrt.shell.text.fba.FbaOptFileLineFormatV1
Returns the header used to indicate the value of the objective function.
getObjValueHeader() - Method in interface sbrt.shell.text.fba.FbaOptHeaderFormatter
Returns the header used to indicate the value of the objective function.
getObjValueHeader() - Method in class sbrt.shell.text.fba.FbaOptHeaderFormatterV1
Returns the header used to indicate the value of the objective function.
getObjValueHeader() - Method in interface sbrt.shell.text.fba.FbaOptHeaderParser
Returns the header used to indicate the value of the objective function.
getObjValueHeader() - Method in class sbrt.shell.text.fba.FbaOptHeaderParserV1
Returns the header used to indicate the value of the objective function.
getOffender() - Method in exception sbrt.kernel.fba.comp.FluxRangeException
Returns the object whose range has exceeded the defined cutoff.
getOptimal(String, OptSense) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the results of computing the optimal flux of the reaction with the provided name.
getOptimal(MathExpr<?>, OptSense) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the results of computing the optimal value of the provided objective function.
getOptimizationSense() - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Returns the current optimization sense.
getOptimizationSense() - Method in class sbrt.kernel.fba.proc.CatalystDeletionProcess
Returns the current optimization sense.
getOptimizationSense() - Method in class sbrt.kernel.fba.proc.CvCatalystDeletionProcess
Returns the current optimization sense.
getOptimizationSense() - Method in class sbrt.kernel.fba.proc.CvFbaOptProcess
Returns the current optimization sense.
getOptimizationSense() - Method in class sbrt.kernel.fba.proc.CvObjectiveFunctionProcess
Returns the current optimization sense.
getOptimizationSense() - Method in class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Returns the current optimization sense.
getOptimizationSense() - Method in class sbrt.kernel.fba.proc.FbaOptProcess
Returns the current optimization sense.
getOptimizationSense() - Method in class sbrt.kernel.fba.proc.ObjFunAnalysis
Returns the current optimization sense.
getOptimizationSense() - Method in class sbrt.kernel.fba.proc.RxnDeletionProcess
Returns the current optimization sense.
getOptionalKeys() - Method in class plug_in_example.shell.GreetingManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.algebra.LinearCombConverterManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.algebra.LinearSolverManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.algebra.MatrixConverterManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.algebra.MultipleVectorsConverterManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.algebra.SingleVectorConverterManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.comb.SingleElementUnionManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.comb.StrictSingleElementUnionManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.BiggSbmlReaderManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.CatalystDeletionManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.CvCatalystDeletionManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.CvFbaOptManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.CvMsFluxIntervalManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.CvObjectiveFunctionManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.CvRevRxnFluxIntervalManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.CvRxnDeletionManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.CvSimpleFluxIntervalManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.ExtremeCurrentManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.FbaOptManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.FbaSolverManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.FluxActivityManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.FluxCapManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.FluxPlasticityManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.InitialPointManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.MetatoolInputReaderManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.MetatoolInputWriterManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.MetatoolOutputReaderManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.MsFluxIntervalManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.MsFluxomeReducerManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.NetworkInfoManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.ObjectiveFunctionManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.PalssonSbmlReaderManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.RandomConstraintsManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.RandomObjectiveManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.RedundRxnRemoverManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.ReverseRxnFluxIntervalManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.RevRxnBreakerManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.RxnDeletionManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.SimpleRxnFileTransManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.SlpCycleIdManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.fba.WwFluxomeReducerManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.geom.CdHarManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.graph_theory.CycleIdManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.graph_theory.GraphInfoManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.graph_theory.PathIdManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.graph_theory.UniqueCycleIdManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in interface sbrt.shell.mng.ProcessManager
Returns the set of keys the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.stat.CorrelationManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.stat.KendallTauManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.stat.MannWhitneyUManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.utilities.IntervalComparisonManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalKeys() - Method in class sbrt.shell.mng.utilities.VariableParticipationManager
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
getOptionalKeys() - Method in class sbrt.shell.mng.utilities.VectorComparisonManager
Returns the set of keywords understood, but not required, by this process manager.
getOptionalValue(Object) - Method in class sbrt.shell.io.ProcessInputFile
Returns the value corresponding to the provided key.
getOptionalValue(Object) - Method in interface sbrt.shell.mng.ManagerInput
Returns the value corresponding to the provided key.
getOptionalValue(Object) - Method in class sbrt.shell.mng.MapManagerInput
Returns the value corresponding to the provided key.
getOptSense(ManagerInput<String, String>) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Parses and returns the value for FbaOptManager.OPTIMIZATION_SENSE in the provided manager input.
getOriginalName() - Method in class sbrt.shell.io.AbstractMapInputFile
Returns the name of this file.
getOriginalName() - Method in class sbrt.shell.io.AbstractMapOutputFile
Returns the name of this file.
getOriginalName() - Method in class sbrt.shell.io.fba.ColumnOrFbaOptOutputFile
Returns the provided name of this file.
getOriginalName() - Method in class sbrt.shell.io.fba.FluxCapInputFile
Returns the provided name of this file.
getOriginalName() - Method in class sbrt.shell.io.fba.FluxIntervalInputFile
Returns the provided name of this file.
getOriginalName() - Method in class sbrt.shell.io.fba.RowOrFbaOptOutputFile
Returns the provided name of this file.
getOriginalName() - Method in class sbrt.shell.io.fba.SerFbaOptOutputFile
Returns the provided name of this file.
getOriginalName() - Method in interface sbrt.shell.io.SbrtFile
Returns the original name given to this file.
getOriginalName() - Method in class sbrt.shell.io.SerializedInputFile
Returns the original name given to this file object.
getOriginalName() - Method in class sbrt.shell.io.SerializedOutputFile
Returns the name of this file.
getOriginalName() - Method in class sbrt.shell.io.TextInputFile
Returns the name of this file.
getOriginalName() - Method in class sbrt.shell.io.TextOutputFile
Returns the name of this file.
getOutputFile(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.comb.SingleElementUnionManager
Returns an output file with the name provided in the manager input.
getOutputFile(String, PrintWriter) - Static method in class sbrt.shell.mng.comb.SingleElementUnionManager
Returns an output file with the provided name.
getOutputFile(String) - Static method in class sbrt.shell.mng.comb.SingleElementUnionManager
Returns an output file with the provided name.
getOutputFile(ManagerInput<String, String>, PrintWriter, Fluxome, Set<String>) - Static method in class sbrt.shell.mng.fba.ExtremeCurrentManager
Returns an output file to which extreme currents can be written.
getOutputFile(String, PrintWriter, Fluxome, Set<String>) - Static method in class sbrt.shell.mng.fba.ExtremeCurrentManager
Returns an output file to which extreme currents can be written.
getOutputFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.RandomConstraintsManager
Returns an empty output file that is suitable for storing multiple sets of flux constraints.
getOutputFile(String, FileFormat, Set<String>, Fluxome) - Static method in class sbrt.shell.mng.fba.RandomConstraintsManager
Returns an empty output file that is suitable for storing multiple sets of flux constraints.
getOutputFile(String, Set<String>, IrrevRxnFluxome) - Static method in class sbrt.shell.mng.fba.RandomConstraintsManager
Returns an empty output file that is suitable for storing multiple sets of flux constraints.
getOutputFile(String, FileFormat, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.RandomObjectiveManager
Returns an empty output file that is suitable for storing randomly generated objective functions.
getOutputFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.RandomObjectiveManager
Returns an empty output file that is suitable for storing randomly generated objective functions.
getOutputFile(String) - Static method in class sbrt.shell.mng.fba.WwFluxomeReducerManager
Returns a file to which the chemical reactions of a fluxome can be written.
getOutputFile(String, PrintWriter) - Static method in class sbrt.shell.mng.fba.WwFluxomeReducerManager
Returns a file to which the chemical reactions of a fluxome can be written.
getOutputFile(ManagerInput<String, String>, PrintWriter, Set<String>) - Static method in class sbrt.shell.mng.geom.CdHarManager
Returns an output file with the name provided in the manager input.
getOutputFile(String, PrintWriter, Set<String>) - Static method in class sbrt.shell.mng.geom.CdHarManager
Returns an output file with the provided name.
getOutputFile(String, Set<String>) - Static method in class sbrt.shell.mng.geom.CdHarManager
Returns an output file with the provided name.
getOutputFile(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.graph_theory.CycleIdManager
Creates a returns an output file if one is specified in the provided input.
getOutputFile(ManagerInput<String, String>) - Static method in class sbrt.shell.mng.graph_theory.CycleIdManager
Creates a returns an output file if one is specified in the provided input.
getOutputRxnFormat() - Method in class sbrt.shell.proc.fba.SimpleRxnFileReader
Returns the formatter used for writing reactions to the output file.
getP() - Method in class sbrt.ext.R.stat.RCorrelator.Result
Returns the corresponding P value.
getPaths() - Method in class sbrt.kernel.math.graph_theory.comp.PathFinder
Returns a list of all paths.
getPaths(Collection<? extends N>, Collection<? extends N>) - Method in class sbrt.kernel.math.graph_theory.comp.PathFinder
Returns a list of all paths between the provided source and sink nodes.
getPaths(T, S) - Method in class sbrt.kernel.math.graph_theory.comp.PathFinder
Returns a list of all paths between the provided source and sink nodes.
getPAvg() - Method in class sbrt.kernel.fba.comp.InitialPointComputer.Results
Returns the average value of all created positioning variables.
getPIntercept() - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Returns the value of each positioning variable at the edges of the convex polytope.
getPIntercept(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.InitialPointManager
Returns the parsed value for InitialPointManager.P_MAX in the provided input.
getPipeSetFormat() - Method in class sbrt.shell.text.fba.FbaOptHeaderFormatterV1
Returns the format used for sets of strings.
getPipeSetFormat() - Method in class sbrt.shell.text.fba.FbaOptHeaderParserV1
Returns the format used for sets of strings.
getPlainWriter() - Method in class sbrt.shell.gui.SbrtOutputPane
Returns the print writer used for writing plain text to the output pane.
getPlane() - Method in class sbrt.kernel.math.geom.ParallelHyperplanes
Returns the hyperplane.
getPlanes(String, PrintWriter) - Static method in class sbrt.shell.mng.geom.CdHarManager
Returns the list of sets contained in the file with the provided name.
getPlanes(String) - Static method in class sbrt.shell.mng.geom.CdHarManager
Returns the list of sets contained in the file with the provided name.
getPlanes(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.geom.CdHarManager
Returns the list of sets contained in the file with the name contained in the provided input.
getPMin() - Method in class sbrt.kernel.fba.comp.InitialPointComputer.Results
Returns the minimum value of the linear combination of all created positioning variables.
getPoint() - Method in class sbrt.kernel.math.geom.comp.CdHarComp.Results
Returns the random interior point that was computed.
getPoint() - Method in exception sbrt.kernel.math.InvalidPointException
Returns the invalid point.
getPointsPerPoint() - Method in class sbrt.kernel.fba.proc.CdHarFluxVectorProcess
Returns the number of points generated per points returned.
getPointsPerPoint(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.geom.CdHarManager
Parses and returns the value for CdHarManager.POINTS_PER_POINT in the provided manager input.
getPolytope() - Method in class sbrt.kernel.math.geom.comp.CdHarComp
Returns the convex polytope for which random points are generated.
getPotActive() - Method in class sbrt.kernel.fba.proc.FluxPlasticityProcess.Results
Returns the set of fluxes that are potentially active.
getPotentiallyActive(Map<String, Interval>, double) - Method in class sbrt.kernel.fba.analysis.FluxIntervalAnalyzer
Returns the potentially-active fluxes in the provided map.
getPredecessors(Object) - Method in class sbrt.kernel.math.graph_theory.DirectedGraph
Returns the predecessors of the provided node.
getProcess() - Method in class plug_in_example.shell.GreetingManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.algebra.LinearSolverManager
Returns the process controlled by this process manager.
getProcess() - Method in class sbrt.shell.mng.comb.SingleElementUnionManager
Returns the process controlled by this process manager.
getProcess() - Method in class sbrt.shell.mng.comb.StrictSingleElementUnionManager
Returns the process controlled by this process manager.
getProcess() - Method in class sbrt.shell.mng.fba.CatalystDeletionManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.CvCatalystDeletionManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.CvFbaOptManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.CvMsFluxIntervalManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.CvObjectiveFunctionManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.CvRevRxnFluxIntervalManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.CvRxnDeletionManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.CvSimpleFluxIntervalManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.ExtremeCurrentManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.FbaOptManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.FbaSolverManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.FluxActivityManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.FluxCapManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.FluxPlasticityManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.InitialPointManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.MsFluxIntervalManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.MsFluxomeReducerManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.NetworkInfoManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.ObjectiveFunctionManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.RandomConstraintsManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.RandomObjectiveManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.RedundRxnRemoverManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.ReverseRxnFluxIntervalManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.RevRxnBreakerManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.RxnDeletionManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.SlpCycleIdManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.fba.WwFluxomeReducerManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.geom.CdHarManager
Returns the process controlled by this process manager.
getProcess() - Method in class sbrt.shell.mng.graph_theory.CycleIdManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.graph_theory.PathIdManager
Returns the process this process manager controls.
getProcess() - Method in interface sbrt.shell.mng.KernelProcessManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.stat.CorrelationManager
Returns the process controlled by this process manager.
getProcess() - Method in class sbrt.shell.mng.stat.KendallTauManager
Returns the process controlled by this process manager.
getProcess() - Method in class sbrt.shell.mng.stat.MannWhitneyUManager
Returns the process controlled by this process manager.
getProcess() - Method in class sbrt.shell.mng.utilities.IntervalComparisonManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.utilities.VariableParticipationManager
Returns the process this process manager controls.
getProcess() - Method in class sbrt.shell.mng.utilities.VectorComparisonManager
Returns the process managed by this object.
getProducts() - Method in class sbrt.kernel.fba.AbstractExchangeRxn
Returns an empty linear combination.
getProducts() - Method in class sbrt.kernel.fba.AbstractRxn
Returns the products of this reaction.
getProducts() - Method in interface sbrt.kernel.fba.ChemRxn
Returns the products of this chemical reaction.
getProducts() - Method in class sbrt.kernel.fba.RevExchRxn
Returns a linear combination representing the products of this exchange reaction.
getProducts() - Method in class sbrt.kernel.fba.SourceRxn
Returns a single-term linear combination.
getProducts(Node) - Method in class sbrt.shell.text.fba.BiggRxnNodeParser
Returns the products of the provided reaction node.
getProducts(Node) - Method in class sbrt.shell.text.fba.PalssonRxnNodeParser
Returns the products of the provided reaction node.
getProgramSolverType() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the Class of the program solver used by this optimization computer.
getProgress() - Method in interface sbrt.kernel.fba.comp.CycleComputer
Returns a progress monitor for this cycle computer.
getProgress() - Method in interface sbrt.kernel.fba.comp.ExtremeCurrentComputer
Returns a progress monitor for this extreme current computer.
getProgress() - Method in class sbrt.kernel.fba.comp.FluxCapComputer
Returns a progress monitor for this flux cap computer.
getProgress() - Method in interface sbrt.kernel.fba.comp.FluxIntervalComputer
Returns a progress monitor for this flux interval computer.
getProgress() - Method in interface sbrt.kernel.fba.comp.FluxomeReducer
Returns a progress monitor for this fluxome reducer.
getProgress() - Method in class sbrt.kernel.fba.comp.MsFluxIntervalComputer
Returns a progress monitor for this flux interval computer.
getProgress() - Method in class sbrt.kernel.fba.comp.MsFluxomeReducer
Returns a progress monitor for this fluxome reducer.
getProgress() - Method in class sbrt.kernel.fba.comp.ReverseRxnIntervalComp
Returns a progress monitor for this flux interval computer.
getProgress() - Method in class sbrt.kernel.fba.comp.SimpleFluxIntervalComputer
Returns a progress monitor for this flux interval computer.
getProgress() - Method in class sbrt.kernel.fba.comp.SlpCycleComputer
Returns a progress monitor for this steady state cycle computer.
getProgress() - Method in class sbrt.kernel.fba.comp.SlpExCurrComputerV2
Returns a progress monitor for this extreme current computer.
getProgress() - Method in class sbrt.kernel.fba.comp.WwFluxomeReducer
Returns a progress monitor for this fluxome reducer.
getProgress() - Method in class sbrt.kernel.fba.proc.CatalystDeletionProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.CdHarFluxVectorProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.CvCatalystDeletionProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.CvFbaOptProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.CvFluxIntervalProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.CvObjectiveFunctionProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.CycleIdProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.ExtremeCurrentProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.FluxActivityProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.FluxCapProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.FluxIntervalProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.FluxomeReducerProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.FluxPlasticityProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.ObjFunAnalysis
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.RandomObjectiveGenerator
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.RxnDeletionProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.SvCdHarFluxVectorProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.fba.proc.SvInitialPointProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.math.geom.proc.CdHarProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.math.graph_theory.proc.CycleIdProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.math.graph_theory.proc.PathIdProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.math.stat.proc.MultipleCorrelationAnalysis
Returns a progress monitor for this process.
getProgress() - Method in interface sbrt.kernel.MonitoredProcess
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.utilities.DiscreteProgressMonitor
Returns an integer value indicating a progress.
getProgress() - Method in class sbrt.kernel.utilities.PercentProgressMonitor
Returns a double precision number indicating the completed percentage of the process being monitored.
getProgress() - Method in class sbrt.kernel.utilities.proc.IntervalComparison
Returns a progress monitor for this process.
getProgress() - Method in class sbrt.kernel.utilities.proc.VectorComparison
Returns a progress monitor for this process.
getProgress() - Method in interface sbrt.kernel.utilities.ProgressMonitor
Returns a number indicating the progress of the process being monitored.
getProteins(Node) - Method in class sbrt.shell.text.fba.PalssonRxnNodeParser
Calls PalssonRxnNodeParser.getCatalysts(Node, String) with "PROTEIN_ASSOCIATION:" as the prefix.
getPVector() - Method in class sbrt.kernel.fba.comp.InitialPointComputer.Results
Returns the vector of values of all positioning variables that were created.
getPVectorFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.InitialPointManager
Returns an empty output file that is suitable for storing a single C vector with the name denoted by InitialPointManager.P_VECTOR_FILE_NAME in the provided input.
getRange() - Method in class sbrt.kernel.math.Interval
Returns getUpper() - getLower().
getRangeCutoff() - Method in exception sbrt.kernel.fba.comp.FluxRangeException
Returns the defined range cutoff.
getReactants() - Method in class sbrt.kernel.fba.AbstractExchangeRxn
Returns an empty linear combination.
getReactants() - Method in class sbrt.kernel.fba.AbstractRxn
Returns the reactants of this reaction.
getReactants() - Method in interface sbrt.kernel.fba.ChemRxn
Returns the reactants of this chemical reaction.
getReactants() - Method in class sbrt.kernel.fba.RevExchRxn
Returns a linear combination representing the reactants of this exchange reaction.
getReactants() - Method in class sbrt.kernel.fba.SinkRxn
Returns a single-term linear combination.
getReactants(Node) - Method in class sbrt.shell.text.fba.BiggRxnNodeParser
Returns the reactants of the provided reaction node.
getReactants(Node) - Method in class sbrt.shell.text.fba.PalssonRxnNodeParser
Returns the reactants of the provided reaction node.
getReactioName() - Method in exception sbrt.kernel.fba.comp.FluxCapException
Returns the name of the reaction whose flux was intended to be capped.
getRegex() - Method in class sbrt.shell.text.AbstractLinkedHashSetFormat
Returns the regular expression used to separate elements when parsing a formatted string.
getRegex() - Method in class sbrt.shell.text.AbstractListFormat
Returns the regular expression used to separate elements when parsing a formatted string.
getRequiredKeys() - Method in class plug_in_example.shell.GreetingManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.io.AbstractMapInputFile
Returns the set of keys that must be contained in this file.
getRequiredKeys() - Method in class sbrt.shell.mng.algebra.LinearCombConverterManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.algebra.LinearSolverManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.algebra.MatrixConverterManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.algebra.MultipleVectorsConverterManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.algebra.SingleVectorConverterManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.comb.SingleElementUnionManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.comb.StrictSingleElementUnionManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.BiggSbmlReaderManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.CatalystDeletionManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.CvCatalystDeletionManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.CvFbaOptManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.CvMsFluxIntervalManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.CvObjectiveFunctionManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.CvRevRxnFluxIntervalManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.CvRxnDeletionManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.CvSimpleFluxIntervalManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.ExtremeCurrentManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.FbaOptManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.FbaSolverManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.FluxActivityManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.FluxCapManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.FluxPlasticityManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.InitialPointManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.MetatoolInputReaderManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.MetatoolInputWriterManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.MetatoolOutputReaderManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.MsFluxIntervalManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.MsFluxomeReducerManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.NetworkInfoManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.ObjectiveFunctionManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.PalssonSbmlReaderManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.RandomConstraintsManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.RandomObjectiveManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.RedundRxnRemoverManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.ReverseRxnFluxIntervalManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.RevRxnBreakerManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.RxnDeletionManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.SimpleRxnFileTransManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.SlpCycleIdManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.fba.WwFluxomeReducerManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.geom.CdHarManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.graph_theory.CycleIdManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.graph_theory.GraphInfoManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.graph_theory.PathIdManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.graph_theory.UniqueCycleIdManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in interface sbrt.shell.mng.ProcessManager
Returns the set of keys the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.stat.CorrelationManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.stat.KendallTauManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.stat.MannWhitneyUManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.utilities.IntervalComparisonManager
Returns the set of keywords required by this process manager.
getRequiredKeys() - Method in class sbrt.shell.mng.utilities.VariableParticipationManager
Returns the set of keywords the provided ManagerInput object must contain.
getRequiredKeys() - Method in class sbrt.shell.mng.utilities.VectorComparisonManager
Returns the set of keywords required by this process manager.
getRequiredValue(Object) - Method in class sbrt.shell.io.ProcessInputFile
Returns the value corresponding to the provided key.
getRequiredValue(Object) - Method in interface sbrt.shell.mng.ManagerInput
Returns the value corresponding to the provided key.
getRequiredValue(Object) - Method in class sbrt.shell.mng.MapManagerInput
Returns the value corresponding to the provided key.
getResults() - Method in class sbrt.kernel.io.ListResultsManager
Returns a copy of the list of results added to this results manager.
getResults() - Method in class sbrt.kernel.io.SingleRm
Returns the last result added to this results manager.
getRevConstraint() - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Returns the constraint used for active reversible reactions.
getRevConstraint(ManagerInput<String, String>) - Static method in class sbrt.shell.mng.fba.RandomConstraintsManager
Parses and returns the value for RandomConstraintsManager.REV_CONSTRAINT in the provided manager input.
getReverseIrrevRxnIds(T, Map<T, IrrevRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns all of the keys in the provided map that correspond to reactions that are the reverse of the reaction specified by the provided key.
getReverseIrrevRxns(T, Map<T, IrrevRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns all of the reactions in the provided map that are the reverse of the reaction specified by the provided key.
getReverseSinkRxnIds(SourceRxn, Map<T, SinkRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns all of the keys in the provided map that correspond to the sink reactions that are the reverse of the provided source reaction.
getReverseSinkRxns(SourceRxn, Map<T, SinkRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns all of the sink reactions in the provided map that are the reverse of the provided source reaction.
getReverseSourceRxnIds(SinkRxn, Map<T, SourceRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns all of the keys in the provided map that correspond to the source reactions that are the reverse of the provided sink reaction.
getReverseSourceRxns(SinkRxn, Map<T, SourceRxn>) - Static method in class sbrt.kernel.fba.RxnComparer
Returns all of the source reactions in the provided map that are the reverse of the provided sink reaction.
getRevRxnFormat() - Method in class sbrt.shell.text.fba.RxnFormatV1
Returns the format used for reversible reactions.
getRightPadding() - Method in class sbrt.shell.text.AbstractMapEntryFormat
Returns the right padding used to create formatted string representations of key-value pairs.
getRow(Object) - Method in interface sbrt.kernel.math.algebra.DoubleMatrix
Returns the row corresponding to the provided row index.
getRow(Object) - Method in class sbrt.kernel.math.algebra.DoubleMatrixWrap
Returns the row corresponding to the provided row index.
getRow(Object) - Method in class sbrt.kernel.math.algebra.HashMatrix
Returns the row corresponding to the provided row index.
getRow(Object) - Method in interface sbrt.kernel.math.algebra.Matrix
Returns the row corresponding to the provided row index.
getRow(Object) - Method in class sbrt.kernel.math.algebra.MatrixWrap
Returns the row corresponding to the provided row index.
getRow(Object) - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Returns the row corresponding to the provided row index.
getRow(Object) - Method in interface sbrt.kernel.math.algebra.SparseDoubleMatrix
Returns the row corresponding to the provided row index.
getRow(Object) - Method in class sbrt.kernel.math.algebra.SparseDoubleMatrixWrap
Returns the row corresponding to the provided row index.
getRow(Object) - Method in class sbrt.kernel.math.algebra.TreeMatrix
Returns the row corresponding to the provided row index.
getRowConstraint(Object) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the current constraint on the provided row variable.
getRowConstraints() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns all the current constraints on row variables.
getRowHeaders() - Method in class sbrt.shell.io.fba.RowOrFbaOptOutputFile
Returns the set of row headers whose values will be written to this output file when results are added.
getRowIndex() - Method in class sbrt.kernel.math.algebra.IndexPair
Returns the row index.
getRowIndex() - Method in class sbrt.kernel.math.algebra.MatrixElement
Returns the row index of this matrix element.
getRowIndexFormat() - Method in class sbrt.shell.text.math.IndexPairFormatV1
Returns the format used for row indices.
getRowIndices() - Method in class sbrt.kernel.math.algebra.HashMatrix
Returns the set of row indices contained in this matrix.
getRowIndices() - Method in interface sbrt.kernel.math.algebra.Matrix
Returns the set of row indices contained in this matrix.
getRowIndices() - Method in class sbrt.kernel.math.algebra.MatrixWrap
Returns the set of row indices contained in this matrix.
getRowIndices() - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Returns the set of row indices contained in this matrix.
getRowIndices() - Method in class sbrt.kernel.math.algebra.TreeMatrix
Returns the set of row indices contained in this matrix.
getRowIndNzEl(Object) - Method in class sbrt.kernel.math.algebra.HashMatrix
Returns the set of row indices whose elements are nonzero in the column corresponding to the provided index.
getRowIndNzEl(Object) - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Returns the set of row indices whose elements are nonzero in the column corresponding to the provided index.
getRowIndNzEl(Object) - Method in interface sbrt.kernel.math.algebra.SparseDoubleMatrix
Returns the set of row indices whose elements are nonzero in the column corresponding to the provided index.
getRowIndNzEl(Object) - Method in class sbrt.kernel.math.algebra.SparseDoubleMatrixWrap
Returns the set of row indices whose elements are nonzero in the column corresponding to the provided index.
getRowIndNzEl(Object) - Method in class sbrt.kernel.math.algebra.TreeMatrix
Returns the set of row indices whose elements are nonzero in the column corresponding to the provided index.
getRowVariables() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the set of all row variables in the program matrix.
getRxn(String) - Method in interface sbrt.kernel.fba.Fluxome
Returns the chemical reaction in this fluxome with the provided name.
getRxn(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the chemical reaction in this fluxome with the provided name.
getRxn(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the chemical reaction in this fluxome with the provided name.
getRxnExpr(String) - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Converts a reaction name to a single-term linear combination.
getRxnExpr(Collection<String>) - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Converts a collection of reaction names to a linear combination.
getRxnExpr(String) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Converts a reaction name to a single-term linear combination.
getRxnExpr(Collection<String>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Converts a collection of reaction names to a linear combination.
getRxnExprConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Returns the current constraint on the provided expression.
getRxnExprConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Returns the current constraint on the provided expression.
getRxnExprConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the current constraint on the provided expression.
getRxnExprConstraint(MathExpr<String>) - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Returns the current constraint on the provided expression.
getRxnExprConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Returns the current constraint on the provided expression.
getRxnExprConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Returns the constraint on the provided mathematical expression of fluxes.
getRxnExprConstraint(MathExpr<String>) - Method in interface sbrt.kernel.fba.Fluxome
Returns the constraint corresponding to the provided mathematical expression of reaction names.
getRxnExprConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the constraint associated with the expression provided.
getRxnExprConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the constraint associated with the expression provided.
getRxnExprConstraints() - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Returns all current flux expression constraints.
getRxnExprConstraints() - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Returns all current flux expression constraints.
getRxnExprConstraints() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns all current constraints on mathematical expressions of reaction names.
getRxnExprConstraints() - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Returns all current flux expression constraints.
getRxnExprConstraints() - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Returns all current flux expression constraints.
getRxnExprConstraints() - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Returns the set of all constraints on mathematical expressions of fluxes.
getRxnExprs() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the set of all mathematical expressions of reaction names.
getRxnFormat() - Method in class sbrt.shell.text.fba.IrfFormatV1
Returns the format used for reactions.
getRxnFormat() - Method in class sbrt.shell.text.fba.MixedFluxomeFormatV1
Returns the format used for reactions.
getRxnId(Node) - Method in class sbrt.shell.text.fba.BiggRxnNodeParser
Returns the reaction ID of the provided reaction node.
getRxnId(Node) - Method in class sbrt.shell.text.fba.PalssonRxnNodeParser
Returns the reaction ID of the provided reaction node.
getRxnNameChecker() - Method in class sbrt.shell.text.fba.RxnNameExprFormatV1
Returns the reaction name verifier.
getRxnNameChecker() - Method in class sbrt.shell.text.fba.RxnNameListFormatV1
Returns the reaction name verifier.
getRxnNameChecker() - Method in class sbrt.shell.text.fba.RxnNameOrExprFormatV1
Returns the reaction name verifier.
getRxnNameChecker() - Method in class sbrt.shell.text.fba.RxnNameSetFormatV1
Returns the reaction name verifier.
getRxnNameExprFormat(Fluxome) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns the default reaction name expression format.
getRxnNameExprSet() - Method in class sbrt.shell.io.fba.RxnNamExprSetInputFile
Returns the set of reaction name expressions contained in this fle.
getRxnNameFormat() - Method in class sbrt.shell.text.fba.IrfFormatV1
Returns the format used for reaction names.
getRxnNameFormat() - Method in class sbrt.shell.text.fba.MixedFluxomeFormatV1
Returns the format used for reaction names.
getRxnNameHeaders(ManagerInput<String, String>, Fluxome) - Static method in class sbrt.shell.mng.fba.FbaManager
Parses and returns the value for AbstractProcessManager.DATA_HEADERS in the provided manager input.
getRxnNameHeaders(String, Fluxome) - Static method in class sbrt.shell.mng.fba.FbaManager
Parses and returns the set of reaction names contained in the provided string.
getRxnNames() - Method in interface sbrt.kernel.fba.Fluxome
Returns the set of names of all chemical reactions contained in this fluxome.
getRxnNames() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the set of names of all chemical reactions contained in this fluxome.
getRxnNames() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the set of names of all chemical reactions contained in this fluxome.
getRxnNames(Set<String>, CatalyzedFluxome) - Static method in class sbrt.kernel.fba.proc.CatalystDeletionProcess
Returns the set of names of reactions whose activity depends on the provided set of catalysts.
getRxnNames() - Method in class sbrt.kernel.fba.proc.NetworkInfoProcess.Results
Returns the names of all reactions contained in the fluxome.
getRxnNameSetFormat() - Method in class sbrt.shell.text.fba.FbaOptHeaderFormatterV1
Returns the format used for reaction name sets.
getRxnNameSetFormat() - Method in class sbrt.shell.text.fba.FbaOptHeaderParserV1
Returns the format used for reaction name sets.
getRxns() - Method in interface sbrt.kernel.fba.Fluxome
Returns the set of all chemical reactions contained in this fluxome.
getRxns(Collection<String>) - Method in interface sbrt.kernel.fba.Fluxome
Returns the chemical reactions with the provided names.
getRxns() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns all chemical reactions contained in this fluxome.
getRxns(Collection<String>) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the chemical reactions with the provided names.
getRxns() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns all chemical reactions contained in this fluxome.
getRxns(Collection<String>) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the chemical reactions with the provided names.
getS(Map<? extends V, Double>, Map<? extends V, Double>) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the S value of the provided values.
getS(Collection<Double>, Collection<Double>) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the S value of the provided values.
getS(double[], double[]) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the S value of the provided values.
getSafetyLevel(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Parses and returns the value for FbaOptManager.SAFETY_LEVEL in the provided manager input.
getSample(String, PrintWriter) - Static method in class sbrt.shell.mng.stat.MannWhitneyUManager
Returns the list of values contained in the file with the provided name.
getSample(String) - Static method in class sbrt.shell.mng.stat.MannWhitneyUManager
Returns the list of values contained in the file with the provided name.
getSeed(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.AbstractProcessManager
Returns the parsed value for AbstractProcessManager.SEED in the provided input and prints a descriptive message to the provided print writer.
getSense() - Method in exception sbrt.kernel.fba.comp.FbaOptException
Returns the sense, or direction, of the attempted optimization.
getSet() - Static method in class sbrt.shell.text.SpecialChars
Returns a set of the characters contained in this class.
getSetFormat() - Method in class sbrt.shell.text.AbstractMapFormat
Returns the format used for sets of keys.
getSetFormat() - Method in class sbrt.shell.text.AppInputFileLineFormatVersion1
Returns the format used for sets of variables.
getSetFormat() - Method in class sbrt.shell.text.ColonMapFormatV1
Returns the format used for sets of variables.
getSetFormat() - Method in class sbrt.shell.text.EqualsMapFormatV1
Returns the format used for sets of variables.
getSetFormat() - Method in class sbrt.shell.text.fba.CatalystSetFormatV1
Returns the format used for sets of catalyst names.
getSetFormat() - Method in class sbrt.shell.text.fba.ConstraintsFileLineFormatV1
Returns the format used for sets of variables.
getSetFormat() - Method in class sbrt.shell.text.fba.ConstraintsFileLineFormatV2
Returns the format used for sets of variables.
getSetFormat() - Method in class sbrt.shell.text.fba.FluxCapFormatV1
Returns the format used for sets of variables.
getSetFormat() - Method in class sbrt.shell.text.fba.FluxomeSolFileLineFormatV1
Returns the format used for sets of variables.
getSetFormat() - Method in class sbrt.shell.text.fba.FluxVectorFormatV1
Returns the format used for sets of variables.
getSetFormat() - Method in class sbrt.shell.text.fba.IrfFormatV1
Returns the format used for sets of reaction names.
getSetFormat() - Method in class sbrt.shell.text.fba.MixedFluxomeFormatV1
Returns the format used for sets of reaction names.
getSetFormat() - Method in class sbrt.shell.text.fba.RxnNameSetFormatV1
Returns the format used for sets of reaction names.
getSetFormat() - Method in class sbrt.shell.text.SimpleSetFormat
Returns the underlying set format.
getSets(String, PrintWriter) - Static method in class sbrt.shell.mng.comb.SingleElementUnionManager
Returns the list of sets contained in the file with the provided name.
getSets(String) - Static method in class sbrt.shell.mng.comb.SingleElementUnionManager
Returns the list of sets contained in the file with the provided name.
getSets(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.comb.SingleElementUnionManager
Returns the list of sets contained in the file with the name contained in the provided input.
getSingleFluxVectorOutputFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns an empty output file that is suitable for storing a single flux vector.
getSingleFluxVectorOutputFile(String, FileFormat, Set<String>, Fluxome) - Static method in class sbrt.shell.mng.fba.FbaManager
Returns an empty output file that is suitable for storing a single flux vector.
getSingleResultOutputFile(ManagerInput<String, String>, PrintWriter, F) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns an empty output file that is suitable for storing a single FBA optimization result.
getSingleResultOutputFile(String, FileFormat, Set<String>, F) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns an empty output file that is suitable for storing a single FBA optimization result.
getSingleResultOutputFile(ManagerInput<String, String>, PrintWriter, Fluxome) - Static method in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
Returns an empty output file that is suitable for storing a single set of flux interval results.
getSingleResultOutputFile(String, Set<String>, Fluxome) - Static method in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
Returns an empty output file that is suitable for storing a single set of flux interval results.
getSingletonSets(Set<E>) - Method in class sbrt.kernel.math.comb.comp.SingleElementUnionsV1
Returns a set of singleton sets created from the provided set.
getSingletonSets(Set<E>) - Method in class sbrt.kernel.math.comb.comp.SingleElementUnionsV2
Returns a set of singleton sets created from the provided set.
getSingletonSets(Set<E>) - Method in class sbrt.kernel.math.comb.comp.StrictSingleElementUnions
Returns a set of singleton sets created from the provided set.
getSink() - Method in class sbrt.kernel.math.graph_theory.DirectedGraph.Edge
Returns the sink node of this directed edge.
getSinkRxn(String) - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the sink reaction in this fluxome with the provided name.
getSinkRxn(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the sink reaction in this fluxome with the provided name.
getSinkRxnNames() - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the names of all sink reactions in this fluxome.
getSinkRxnNames() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the set of names of all sinks in this fluxome.
getSinkRxns(Collection<String>) - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the sink reactions with the provided names.
getSinkRxns() - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the set of all sink reactions in this fluxome.
getSinkRxns() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns all of the sinks in this fluxome.
getSinkRxns(Collection<String>) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the sink reactions whose names appear in the provided collection of reaction names.
getSmallest(double, double) - Static method in class sbrt.kernel.utilities.Util
Returns the smallest of the provided numbers.
getSmallest(int, int) - Static method in class sbrt.kernel.utilities.Util
Returns the smallest of the provided numbers.
getSolution(Object) - Method in class sbrt.kernel.math.algebra.HashLinearSystemSolution
Returns the linear combination of free variables to which the provided variable is equal.
getSolution(Object) - Method in interface sbrt.kernel.math.algebra.LinearSystemSolution
Returns the linear combination of free variables to which the provided variable is equal.
getSolutionVector() - Method in class sbrt.ext.cplex.CplexSolver
Returns the most recently computed solution vector.
getSolutionVector() - Method in class sbrt.ext.glpk.GlpkSolver
Returns the most recently computed solution vector.
getSolutionVector() - Method in class sbrt.kernel.fba.comp.FbaOptimizer.Results
Returns the solution vector computed during optimization.
getSolutionVector(Map<?, Double>) - Method in class sbrt.kernel.math.algebra.HashLinearSystemSolution
Computes and returns a solution vector by plugging in the provided values for the free variables in this solution.
getSolutionVector(Map<?, Double>) - Method in interface sbrt.kernel.math.algebra.LinearSystemSolution
Computes and returns a solution vector by plugging in the provided values for the free variables in this solution.
getSolutionVector() - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Returns the most recently computed solution vector.
getSolver(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.algebra.LinearSolverManager
Returns the linear system solver specified by LinearSolverManager.KERNEL_LINK_CMD in the provided input.
getSorted(int[]) - Static method in class sbrt.kernel.utilities.Util
Returns a new array containing the values from the provided array in ascending numerical order.
getSorted(double[]) - Static method in class sbrt.kernel.utilities.Util
Returns a new array containing the values from the provided array in ascending numerical order.
getSortedArray(Collection<? extends Number>) - Static method in class sbrt.kernel.utilities.Util
Returns a sorted array containing the values in the provided collection.
getSortedArray(Collection<Integer>) - Static method in class sbrt.kernel.utilities.Util
Returns a sorted array containing the values in the provided collection.
getSource() - Method in class sbrt.kernel.math.graph_theory.DirectedGraph.Edge
Returns the source node of this directed edge.
getSourceRxn(String) - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the source reaction in this fluxome with the provided name.
getSourceRxn(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the source reaction in this fluxome with the provided name.
getSourceRxnNames() - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the names of all source reactions in this fluxome.
getSourceRxnNames() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the set of names of all sources in this fluxome.
getSourceRxns(Collection<String>) - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the source reactions with the provided names.
getSourceRxns() - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns the set of all source reactions in this fluxome.
getSourceRxns() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns all of the sources in this fluxome.
getSourceRxns(Collection<String>) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the source reactions whose names appear in the provided collection of reaction names.
getSpecies() - Method in class sbrt.kernel.fba.AbstractExchangeRxn
Returns the chemical species associated with this exchange reaction.
getSpecies() - Method in interface sbrt.kernel.fba.ExchangeRxn
Returns the chemical species associated with this exchange reaction.
getSpecies() - Method in interface sbrt.kernel.fba.Fluxome
Returns the set of names of all chemical species participating in reactions contained in this fluxome.
getSpecies() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the set of names of all chemical species participating in reactions contained in this fluxome.
getSpecies() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the set of names of all chemical species participating in reactions contained in this fluxome.
getStatistic() - Method in class sbrt.ext.R.stat.RCorrelator.Result
Returns the corresponding statistic.
getStatus() - Method in class sbrt.ext.cplex.CplexSolver
Returns the status of the most recently attempted optimization.
getStatus() - Method in class sbrt.ext.glpk.GlpkSolver
Returns the status of the most recently attempted optimization.
getStatus() - Method in exception sbrt.kernel.fba.comp.FbaOptException
Returns the status of the attempted optimization.
getStatus() - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Returns the status of the most recently attempted optimization.
getStdev() - Method in class sbrt.kernel.math.stat.NormalDist
Returns the standard deviation of this distribution.
getStoichMatrix() - Method in interface sbrt.kernel.fba.Fluxome
Returns the stoichiometry matrix of this fluxome.
getStoichMatrix() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the stoichiometry matrix of this fluxome.
getStoichMatrix() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the stoichiometry matrix of this fluxome.
getStoichMatrix() - Method in class sbrt.kernel.fba.proc.NetworkInfoProcess.Results
Returns the stoichiometry matrix of the fluxome.
getSuccessors(Object) - Method in class sbrt.kernel.math.graph_theory.DirectedGraph
Returns the successors of the provided node.
getSvInputFile(ManagerInput<String, String>, PrintWriter, Fluxome, double) - Static method in class sbrt.shell.mng.fba.IntervalVariationManager
Returns the space variation input with the name denoted by IntervalVariationManager.FLUX_INTERVAL_FILE in the provided manager input.
getT(double, int, int) - Method in class sbrt.kernel.math.stat.comp.MannWhitneyU
Computes and returns an approximate t value for the provided U value.
getTau(double[], double[]) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the correlation statistic for the provided values.
getTau(Map<? extends V, Double>, Map<? extends V, Double>) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the correlation statistic for the provided values.
getTau(Collection<Double>, Collection<Double>) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the correlation statistic for the provided values.
getTau(double[], double[]) - Method in class sbrt.kernel.math.stat.comp.KendallTauA
Computes and returns the correlation statistic for the provided values.
getTau(double[], double[]) - Method in class sbrt.kernel.math.stat.comp.KendallTauB
Computes and returns the correlation statistic for the provided values.
getTermArray() - Method in class sbrt.kernel.math.HashLinearComb
Returns the terms of this linear combination as an array.
getTermArray() - Method in interface sbrt.kernel.math.LinearComb
Returns the terms of this linear combination as an array.
getTermArray() - Method in interface sbrt.kernel.math.Polynomial
Returns an array containing all of the terms of this polynomial.
getTermFormat() - Method in class sbrt.shell.text.math.LinearCombFormatV1
Returns the format used for terms.
getTermFormat() - Method in class sbrt.shell.text.math.LinearCombFormatV2
Returns the format used for terms.
getTermList() - Method in class sbrt.kernel.math.AbstractLinearComb
Returns the terms of this linear combination as list.
getTermList() - Method in interface sbrt.kernel.math.LinearComb
Returns the terms of this linear combination as list.
getTextFileFormat(String) - Static method in class sbrt.shell.mng.AbstractProcessManager
Returns the text file format corresponding to the provided string.
getTextFileFormat(ManagerInput<String, String>) - Static method in class sbrt.shell.mng.AbstractProcessManager
Returns the parsed value for AbstractProcessManager.FILE_FORMAT in the provided input.
getTieScore(Map<? extends V, Double>) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the tie score of the provided values.
getTieScore(Collection<Double>) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the tie score of the provided values.
getTieScore(double[]) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the tie score of the provided values.
getTolerance() - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Returns the constraint tolerance used by this flux interval computer.
getTolerance() - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Returns the constraint tolerance.
getTolerance() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Returns the allowable amount by which column variables may violate their defined constraints.
getTolerance() - Method in interface sbrt.kernel.fba.comp.FluxIntervalComputer
Returns the amount by which constraints can be violated.
getTolerance() - Method in exception sbrt.kernel.fba.comp.InvalidFluxVectorException
Returns the numerical tolerance used to check the validity of the flux vector.
getTolerance() - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Returns the constraint tolerance.
getTolerance() - Method in class sbrt.kernel.math.DoubleEquiv
Returns the tolerance used by this equivalence tester.
getTolerance() - Method in class sbrt.kernel.math.IntervalEquiv
Returns the tolerance used by this equivalence tester.
getTolerance() - Method in class sbrt.kernel.utilities.proc.IntervalComparison
Returns the equivalence tolerance.
getTolerance() - Method in class sbrt.kernel.utilities.proc.VectorComparison
Returns the equivalence tolerance.
getTolerance() - Method in class sbrt.shell.io.fba.FluxIntervalInputFile
Returns the constraint tolerance.
getTotalOps(IrrevRxnFluxome) - Method in interface sbrt.kernel.fba.comp.ExtremeCurrentComputer
Returns the total number of "operations" required to compute the extreme currents of the provided fluxome.
getTotalOps(IrrevRxnFluxome) - Method in class sbrt.kernel.fba.comp.SlpExCurrComputerV2
Returns the total number of "operations" required to compute the extreme currents of the provided fluxome.
getU() - Method in class sbrt.kernel.math.stat.comp.MannWhitneyResults
Returns the computed U statistic.
getU(List<? extends Number>, List<? extends Number>) - Method in class sbrt.kernel.math.stat.comp.MannWhitneyU
Computes and returns the Mann-Whitney U statistic for the provided samples.
getU(int[], int[]) - Method in class sbrt.kernel.math.stat.comp.MannWhitneyU
Computes and returns the Mann-Whitney U statistic for the provided samples.
getU(double[], double[]) - Method in class sbrt.kernel.math.stat.comp.MannWhitneyU
Computes and returns the Mann-Whitney U statistic for the provided samples.
getUnchangedVariables() - Method in class sbrt.kernel.math.geom.comp.CdHarComp.Results
Returns the variables whose values are the same as they were in the previous point.
getUnions(Collection<Set<E>>) - Method in class sbrt.kernel.math.comb.comp.SingleElementUnionsV1
Returns the set of single-element unions of the sets in the provided collection.
getUnions(Collection<Set<E>>) - Method in class sbrt.kernel.math.comb.comp.SingleElementUnionsV2
Returns the set of single-element unions of the sets in the provided collection.
getUnions(Collection<Set<E>>) - Method in class sbrt.kernel.math.comb.comp.StrictSingleElementUnions
Returns the set of strict single-element unions of the sets in the provided collection.
getUpper() - Method in exception sbrt.kernel.math.IllegalBoundsException
Returns the upper bound used to create this exception.
getUpper() - Method in class sbrt.kernel.math.Interval
Returns the upper bound (or endpoint) of this interval.
getUpperBound(Node) - Method in class sbrt.shell.text.fba.BiggRxnNodeParser
Returns the upper flux bound of the provided reaction node.
getUpperBound(Node) - Method in class sbrt.shell.text.fba.PalssonRxnNodeParser
Returns the upper flux bound of the provided reaction node.
getValue() - Method in exception sbrt.kernel.math.ConstraintViolationException
Returns the value that has violated its constraints.
getValue1() - Method in class sbrt.kernel.math.VectorComparer.Diff
Returns the "first" value of the pair of values.
getValue2() - Method in class sbrt.kernel.math.VectorComparer.Diff
Returns the "second" value of the pair of values.
getValueFormat() - Method in class sbrt.shell.text.ColonMapEntryFormatV1
Returns the format used for values.
getValueFormat() - Method in class sbrt.shell.text.EqualsMapEntryFormatV1
Returns the format used for values.
getValueFormatter() - Method in class sbrt.shell.text.AbstractMapFormat
Returns the formatter used for values.
getValueParser() - Method in class sbrt.shell.text.AbstractMapFormat
Returns the parser used for values.
getVariable() - Method in class sbrt.kernel.math.AbstractLinearComb.Term
Returns the variable contained in this term.
getVariable() - Method in exception sbrt.kernel.math.algebra.IllegalFreeVariableException
Returns the illegal free variable.
getVariable() - Method in exception sbrt.kernel.math.ConstraintViolationException
Returns the variable that has violated its constraints.
getVariable() - Method in exception sbrt.kernel.math.IllegalBoundsException
Returns the object with which these illegal bounds are associated.
getVariable() - Method in class sbrt.kernel.math.IntervalComparer.Diff
Returns the variable for which the intervals correspond.
getVariable() - Method in interface sbrt.kernel.math.LinearComb.Term
Returns the variable contained in this term.
getVariable() - Method in exception sbrt.kernel.math.MissingVariableException
Returns the missing variable.
getVariable() - Method in exception sbrt.kernel.math.UnboundedVariableException
Returns the unbounded variable.
getVariable() - Method in class sbrt.kernel.math.VectorComparer.Diff
Returns the variable for which the numerical values correspond.
getVariableFormat() - Method in class sbrt.shell.text.math.LinCombTermFormatV1
Returns the format used for variables.
getVariableFormat() - Method in class sbrt.shell.text.math.LinCombTermFormatV2
Returns the format used for variables.
getVariableFormat() - Method in class sbrt.shell.text.math.LinearCombFormatV1
Returns the format used for variables.
getVariableFormat() - Method in class sbrt.shell.text.math.LinearCombFormatV2
Returns the format used for variables.
getVariables() - Method in class sbrt.kernel.math.AbstractLinearComb.Term
Returns the set of variables contained in this term.
getVariables() - Method in class sbrt.kernel.math.algebra.HashLinearSystemSolution
Returns the set of variables contained in this solution.
getVariables() - Method in interface sbrt.kernel.math.algebra.LinearSystemSolution
Returns the set of variables contained in this solution.
getVariables() - Method in interface sbrt.kernel.math.geom.ConvexPolytope
Returns the variables contained in the hyperplanes defining the bounding half-spaces.
getVariables() - Method in class sbrt.kernel.math.geom.HashConvexPolytope
Returns the variables contained in the hyperplanes defining the bounding half-spaces.
getVariables() - Method in class sbrt.kernel.math.HashLinearComb
Returns the set of variables contained in this mathematical expression.
getVariables() - Method in interface sbrt.kernel.math.MathExpr
Returns the set of variables contained in this mathematical expression.
getVariables() - Method in interface sbrt.kernel.math.Polynomial.Term
Returns the set of variables contained in this term.
getVariance() - Method in class sbrt.kernel.math.stat.NormalDist
Returns the variance of this distribution.
getVarS(Map<? extends V, Double>, Map<? extends V, Double>) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the variance of S for the provided values.
getVarS(Collection<Double>, Collection<Double>) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the variance of S for the provided values.
getVarS(double[], double[]) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the variance of S for the provided values.
getVector(String) - Static method in class sbrt.shell.mng.stat.CorrelationManager
Parses the file with the provided name and returns the vector it contains.
getVector(String, PrintWriter) - Static method in class sbrt.shell.mng.stat.CorrelationManager
Parses the file with the provided name, prints a status message to the provided print writer, and returns the vector the file contains.
getVersion() - Static method in class sbrt.Sbrt
Returns the full version number of the Systems Biology Research Tool.
getWriter() - Static method in class sbrt.shell.io.DevNull
Returns an instance of this class wrapped by a print writer.
getXValues(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.stat.CorrelationManager
Returns the parsed value for CorrelationManager.X_FILE_NAME in the provided input and prints a descriptive message to the provided print writer.
getYValues(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.stat.CorrelationManager
Returns the parsed value for CorrelationManager.Y_FILE_NAME in the provided input and prints a descriptive message to the provided print writer.
getZeroCutoff() - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Returns the zero cutoff used by this flux interval computer.
getZeroCutoff() - Method in interface sbrt.kernel.fba.comp.FluxIntervalComputer
Returns the current zero cutoff.
getZeroCutoff() - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Returns the zero cutoff.
getZeroCutoff() - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Returns the current zero cutoff.
getZeroCutoff() - Method in class sbrt.kernel.fba.proc.CatalystDeletionProcess
Returns the current zero cutoff used by the reaction deletion computer.
getZeroCutoff() - Method in class sbrt.kernel.fba.proc.CvCatalystDeletionProcess
Returns the current zero cutoff used by the reaction deletion computer.
getZeroCutoff() - Method in class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Returns the current zero cutoff used by the reaction deletion computer.
getZeroCutoff() - Method in class sbrt.kernel.fba.proc.RxnDeletionProcess
Returns the current zero cutoff used by the reaction deletion computer.
getZeroCutoff() - Method in class sbrt.kernel.math.AbstractLinearComb
Returns the current zero cutoff.
getZeroCutoff() - Method in interface sbrt.kernel.math.LinearComb
Returns the current zero cutoff.
getZeroCutoff(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.mng.AbstractProcessManager
Returns the parsed value for AbstractProcessManager.ZERO_CUTOFF in the provided input.
getZeroCutoff(ManagerInput<String, String>) - Static method in class sbrt.shell.mng.AbstractProcessManager
Returns the parsed value for AbstractProcessManager.ZERO_CUTOFF in the provided input.
GLPK - Static variable in class sbrt.shell.ProgramSolverFactory
The string used to denote the GLPK program solver from GNU.
GlpkSolver<R,C> - Class in sbrt.ext.glpk
This class is a wrapper for the GLPK package from GNU.
GlpkSolver() - Constructor for class sbrt.ext.glpk.GlpkSolver
Constructs a new GLPK program solver.
GraphInfoManager - Class in sbrt.shell.mng.graph_theory
This class is used to manage a graph information gatherer.
GraphInfoManager() - Constructor for class sbrt.shell.mng.graph_theory.GraphInfoManager
 
GREATER_THAN - Static variable in class sbrt.shell.text.SpecialChars
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GreetingManager - Class in plug_in_example.shell
This class is used to manage greeting processes.
GreetingManager() - Constructor for class plug_in_example.shell.GreetingManager
 
GreetingProcess - Class in plug_in_example.kernel
This class is used to issue random greetings.
GreetingProcess(long) - Constructor for class plug_in_example.kernel.GreetingProcess
Constructs a new greeting process.
GUI_ARG - Static variable in class sbrt.Sbrt
The argument used to launch the GUI from the command line.
GZIP_SER - Static variable in class sbrt.shell.io.FileFormat
Used to denote a file containing serialized objects that has been compressed using the GNU program gzip.
GZIP_TEXT - Static variable in class sbrt.shell.io.FileFormat
Used to denote a plain-text file that has been compressed using the GNU program gzip.

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