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

C

CARET - Static variable in class sbrt.shell.text.SpecialChars
^
CAT - Static variable in class sbrt.shell.proc.fba.MetatoolInputReader
The Metatool keyword -CAT.
CATALYST_DELETION_FILE - Static variable in class sbrt.shell.mng.fba.CatalystDeletionManager
The keyword used to denote the name of a file containing sets of names of catalysts whose effect upon deletion will be computed.
CATALYST_FILE_NAME - Static variable in class sbrt.shell.mng.fba.NetworkInfoManager
The keyword used to denote teh name of the file to which all catalysts will be written.
CatalystDeletionManager - Class in sbrt.shell.mng.fba
This class is used to manage FBA catalyst deletion processes.
CatalystDeletionManager() - Constructor for class sbrt.shell.mng.fba.CatalystDeletionManager
 
CatalystDeletionProcess<F extends CatalyzedFluxome> - Class in sbrt.kernel.fba.proc
This class is used to perform catalyst deletion processes.
CatalystDeletionProcess(RxnDeletionComputer<F>) - Constructor for class sbrt.kernel.fba.proc.CatalystDeletionProcess
Constructs a new catalyst deletion process.
CatalystFormat - Interface in sbrt.shell.text.chem
This interface is used to represent the formats of catalysts in chemical reactions.
CatalystFormatV1 - Class in sbrt.shell.text.chem
This class is a concrete implementation of CatalystFormat.
CatalystFormatV1() - Constructor for class sbrt.shell.text.chem.CatalystFormatV1
 
CatalystFormatV2 - Class in sbrt.shell.text.chem
This class is a concrete implementation of CatalystFormat.
CatalystFormatV2() - Constructor for class sbrt.shell.text.chem.CatalystFormatV2
 
CatalystListFormat - Interface in sbrt.shell.text.fba
This interface is used to represent the formats of lists of catalyst names.
CatalystListFormatV1 - Class in sbrt.shell.text.fba
This class is a concrete implemenation of CatalystListFormat.
CatalystListFormatV1(CatalyzedFluxome) - Constructor for class sbrt.shell.text.fba.CatalystListFormatV1
Constructs a new catalyst name collection format using the provided fluxome.
catalysts() - Method in interface sbrt.kernel.fba.CatalyzedFluxome
Returns the total number of catalysts contained in this fluxome.
catalysts() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the total number of catalysts contained in this fluxome.
catalysts() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the total number of catalysts contained in this fluxome.
CatalystSetFormat - Interface in sbrt.shell.text.fba
This interface is used to represent the formats of sets of enzyme names.
CatalystSetFormatV1 - Class in sbrt.shell.text.fba
This class is a concrete implemenation of CatalystSetFormat.
CatalystSetFormatV1(CatalyzedFluxome) - Constructor for class sbrt.shell.text.fba.CatalystSetFormatV1
Constructs a new catalyst name collection format using the provided fluxome.
CatalystVerifier - Class in sbrt.shell.text.fba
This class is used to ensure catalysts exist in a given CatalyzedFluxome.
CatalystVerifier(CatalyzedFluxome) - Constructor for class sbrt.shell.text.fba.CatalystVerifier
Constructs a new catalyst name verifier for the provided fluxome.
CatalyzedFluxome - Interface in sbrt.kernel.fba
This interface is used to represent fluxomes with catalyzed reactions.
CdHarComp<V> - Class in sbrt.kernel.math.geom.comp
This class is an implemenation of a coordinate-direction hit-and-run algorithm.
CdHarComp(ConvexPolytope<V>) - Constructor for class sbrt.kernel.math.geom.comp.CdHarComp
Constructs a new random point generator for the provided convex polytope.
CdHarComp.Results - Class in sbrt.kernel.math.geom.comp
This class is used to represent the results of a random point computation.
CdHarFluxComp<F extends Fluxome> - Class in sbrt.kernel.fba.comp
This class is used to compute randomly distributed vectors within flux space.
CdHarFluxComp(F, LinearSystemSolution<String>) - Constructor for class sbrt.kernel.fba.comp.CdHarFluxComp
Constructs a new random flux vector computer for the provided fluxome.
CdHarFluxComp.Results - Class in sbrt.kernel.fba.comp
This class is used to represent the results of a coordinate-direction hit-and-run flux vector computation.
CdHarFluxVectorManager - Class in sbrt.shell.mng.fba
This class is used to manage FBA coordinate direction hit-and-run random flux vector processes.
CdHarFluxVectorManager() - Constructor for class sbrt.shell.mng.fba.CdHarFluxVectorManager
 
CdHarFluxVectorProcess<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to perform coordinate direction hit-and-run flux vector processes.
CdHarFluxVectorProcess(CdHarFluxComp<F>) - Constructor for class sbrt.kernel.fba.proc.CdHarFluxVectorProcess
Constructs a new coordinate direction hit-and-run flux vector process.
CdHarManager - Class in sbrt.shell.mng.geom
This class is used to manage coordinate direction hit-and-run algorithms.
CdHarManager() - Constructor for class sbrt.shell.mng.geom.CdHarManager
 
CdHarProcess<V> - Class in sbrt.kernel.math.geom.proc
This class is used to generate random, uniformly distributed points from the interior of a convex polytope.
CdHarProcess(ConvexPolytope<V>) - Constructor for class sbrt.kernel.math.geom.proc.CdHarProcess
Constructs a new random point generator process for the provided polytope.
changedVariables() - Method in class sbrt.kernel.math.geom.comp.CdHarComp.Results
Returns the number of variables whose values are different than they were in the previous point.
check(ManagerInput<String, String>) - Method in class sbrt.shell.mng.AbstractProcessManager
Throws an ApplicationException if this ProcessManager cannot understand the provided input.
check(ManagerInput<K, V>) - Method in interface sbrt.shell.mng.ProcessManager
Throws an ApplicationException if this ProcessManager cannot understand the provided input.
checkCatalyst(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Ensures the provided string is a valid catalyst.
checkCatalyst(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Ensures the provided string is a valid catalyst.
checkChemSpecies(String) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures the provided string is the name of a chemical species in the fluxome used by this optimization computer.
checkColExpr(MathExpr<?>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures all the variables in the provided expression are valid column variables.
checkColumnValue(Object, Double) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures the provided numerical value does not violate the defined constraint of the provided column variable.
checkColumnValue(Object, double) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures the provided numerical value does not violate the defined constraint of the provided column variable.
checkColumnVariable(Object) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures the provided object is column variable.
checkColumnVariables(Collection<?>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures each element of the provided collection is column variable.
checkConstant(double) - Static method in class sbrt.kernel.math.AbstractPolynomial
Ensures the provided constant is not infinite and not NaN.
checkFile(String) - Static method in class sbrt.shell.io.FileLineIterator
Ensures the provided string is the name of a valid file.
checkFluxConstraint(Interval, String, double) - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Ensures the flux constraint is valid for the fluxome provided.
checkFluxConstraint(Interval, String, double) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures the provided constraint is a valid flux constraint in the fluxome used by this optimization computer.
checkForConflict(FluxConstraints, Set<String>) - Static method in class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Ensures that the provided flux constraints and set of reaction names do not conflict.
checkNumber(double) - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Ensures the provided number is not NaN or infinite.
checkNumber(double) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures the provided number is finite and not NaN.
checkRowVariable(Object) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures the provided object is row variable.
checkRxnExpr(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Ensures the expression is valid for the fluxome provided.
checkRxnExpr(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures all the variables in the provided expression are reaction names.
checkRxnExprConstraint(Interval) - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Ensures the expression constraint is valid for the fluxome provided.
checkRxnExprConstraint(Interval) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures the provided constraint is valid for reaction name-expressions for the fluxome used by this optimization computer.
checkRxnName(String) - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Ensures the reaction name is valid for the fluxome provided.
checkRxnName(String) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures the provided string is the name of a reaction in the fluxome used by this optimization computer.
checkRxnName(String) - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Ensures the provided string is a valid reaction name.
checkRxnName(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Ensures the provided string is a valid reaction name.
checkRxnName(String) - Method in interface sbrt.kernel.fba.MixedFluxome
Ensures the provided string is a valid reaction name.
checkRxnName(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Ensures the provided string is a valid reaction name.
checkRxnNames(Collection<String>) - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Ensures the reaction names are valid for the fluxome provided.
checkRxnNames(Collection<String>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures each element of the provided collection is reaction name.
checkRxnNames(Collection<String>) - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Ensures each element of the provided collection is a valid reaction name.
checkRxnNames(Collection<String>) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Ensures each element of the provided collection is a valid reaction name.
checkRxnNames(Collection<String>) - Method in interface sbrt.kernel.fba.MixedFluxome
Ensures each element of the provided collection is a valid reaction name.
checkRxnNames(Collection<String>) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Ensures each element of the provided collection is a valid reaction name.
checkSolutionVector(Map<?, Double>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Ensures the provided solution vector does not violate the defined constraints of the system.
checkState() - Method in class sbrt.kernel.io.AbstractResultsManager
Ensures close() has not already been called.
CHEM_SPECIES_FILE_NAME - Static variable in class sbrt.shell.mng.fba.NetworkInfoManager
The keyword used to denote the name of the file to which the chemical species of a fluxome will be written.
ChemRxn - Interface in sbrt.kernel.fba
This interface is used to represent chemical reactions.
ChemSpeciesFormat - Interface in sbrt.shell.text.chem
This interface is used to represent the formats of chemical species.
ChemSpeciesFormatV1 - Class in sbrt.shell.text.chem
This class is a concrete implemenation of ChemSpeciesFormat.
ChemSpeciesFormatV1() - Constructor for class sbrt.shell.text.chem.ChemSpeciesFormatV1
 
ChemSpeciesVerifier - Class in sbrt.shell.text.fba
This class is used to ensure chemical species exist in a given Fluxome.
ChemSpeciesVerifier(Fluxome) - Constructor for class sbrt.shell.text.fba.ChemSpeciesVerifier
Constructs a new chemical species verifier for the provided fluxome.
clear() - Method in class sbrt.ext.cplex.CplexSolver
Clears all information contained in this program solver.
clear() - Method in class sbrt.ext.glpk.GlpkSolver
Clears all information contained in this program solver.
clear() - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Clears all information contained in this program solver.
clear() - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.clear().
clear() - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.clear().
clear() - Method in class sbrt.kernel.utilities.UnmodifiableMap
See Map.clear().
clear() - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.clear().
close() - Method in class sbrt.ext.mma.algebra.MathematicaSolver
Closes the link to the Mathematica kernel.
close() - Method in class sbrt.kernel.io.AbstractResultsManager
Closes this results manager.
close() - Method in interface sbrt.kernel.io.ResultsManager
Closes this results manager so that no further results can be added.
close() - Method in class sbrt.shell.io.AbstractMapInputFile
Closes this file.
close() - Method in class sbrt.shell.io.AbstractMapOutputFile
Closes this file.
close() - Method in class sbrt.shell.io.fba.ColumnOrFbaOptOutputFile
Closes this file.
close() - Method in class sbrt.shell.io.fba.FluxCapInputFile
Closes this file.
close() - Method in class sbrt.shell.io.fba.FluxIntervalInputFile
Closes this file.
close() - Method in class sbrt.shell.io.fba.RowOrFbaOptOutputFile
Closes this file.
close() - Method in class sbrt.shell.io.fba.SerFbaOptOutputFile
Closes this file.
close() - Method in class sbrt.shell.io.MultiOutputFiles
Closes this results manager so that no further results can be added.
close() - Method in interface sbrt.shell.io.SbrtFile
Closes this file.
close() - Method in class sbrt.shell.io.SerializedFileIterator
Closes this file iterator.
close() - Method in class sbrt.shell.io.SerializedInputFile
Closes this file.
close() - Method in class sbrt.shell.io.SerializedOutputFile
Closes this file.
close() - Method in class sbrt.shell.io.TextFileLineIterator
Closes this file iterator.
close() - Method in class sbrt.shell.io.TextInputFile
Closes this file.
close() - Method in class sbrt.shell.io.TextOutputFile
Closes this file.
closeFile(SbrtFile, PrintWriter) - Static method in class sbrt.shell.mng.AbstractProcessManager
Closes the provided results manager and prints a descriptive message to the provided print writer.
closeRm(ResultsManager<?>, PrintWriter) - Static method in class sbrt.shell.mng.AbstractProcessManager
Closes the provided file and prints a descriptive message to the provided print writer.
CoeffFormat - Interface in sbrt.shell.text.math
This interface is used to represent the format of coefficients of mathematical expressions.
CoeffFormatV1 - Class in sbrt.shell.text.math
This class is a concrete implementation of CoeffFormat.
CoeffFormatV1() - Constructor for class sbrt.shell.text.math.CoeffFormatV1
Constructs a new coefficient format object.
CoeffFormatV2 - Class in sbrt.shell.text.math
This class is a concrete implementation of CoeffFormat.
CoeffFormatV2() - Constructor for class sbrt.shell.text.math.CoeffFormatV2
Constructs a new coefficient format object.
CofoofSource<F extends Fluxome> - Class in sbrt.shell.io.fba
This class is used to provide a source of column-oriented FBA optimization output files.
CofoofSource(Iterator<String>, FileFormat, Set<String>, FbaOptFileLineFormat) - Constructor for class sbrt.shell.io.fba.CofoofSource
Constructs a new source of column-oriented FBA optimization output files.
CofoofSource(Iterator<String>, String, FileFormat, Set<String>, FbaOptFileLineFormat) - Constructor for class sbrt.shell.io.fba.CofoofSource
Constructs a new source of column-oriented FBA optimization output files.
CollectionFormat<E> - Interface in sbrt.shell.text
This interface is used to represent collection formats.
COLON - Static variable in class sbrt.shell.text.SpecialChars
:
ColonMapEntryFormatV1<K,V> - Class in sbrt.shell.text
This class is a concrete implementation of MapEntryFormat.
ColonMapEntryFormatV1(SimpleFormat<K>, SimpleFormat<V>) - Constructor for class sbrt.shell.text.ColonMapEntryFormatV1
Constructs a new map entry format using the provided key and value formats.
ColonMapFormatV1<K,V> - Class in sbrt.shell.text
This class is a concrete implementation of MapFormat.
ColonMapFormatV1(SimpleFormat<K>, SimpleFormat<V>) - Constructor for class sbrt.shell.text.ColonMapFormatV1
Constructs a new map format using the provided key and value formats.
ColumnOrFbaOptOutputFile<F extends Fluxome> - Class in sbrt.shell.io.fba
This class is used to write column-oriented output files containing FBA optimization data.
ColumnOrFbaOptOutputFile(String, FileFormat, Set<String>, FbaOptFileLineFormat) - Constructor for class sbrt.shell.io.fba.ColumnOrFbaOptOutputFile
Constructs a new column-oriented FBA optimization output file.
columns() - Method in class sbrt.kernel.math.algebra.HashMatrix
Returns the number of columns in this matrix.
columns() - Method in interface sbrt.kernel.math.algebra.Matrix
Returns the number of columns in this matrix.
columns() - Method in class sbrt.kernel.math.algebra.MatrixWrap
Returns the number of columns in this matrix.
columns() - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Returns the number of columns in this matrix.
columns() - Method in class sbrt.kernel.math.algebra.TreeMatrix
Returns the number of columns in this matrix.
ComiFile<K,V> - Class in sbrt.shell.io
This class is used to read column-oriented map input files.
ComiFile(String, FileFormat, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.ComiFile
Constructs a new row-oriented map input file from the provided arguments.
ComiFile(String, FileFormat, MapFormat<K, V>) - Constructor for class sbrt.shell.io.ComiFile
Constructs a new row-oriented map input file from the provided arguments.
ComiFile(String, MapFormat<K, V>) - Constructor for class sbrt.shell.io.ComiFile
Constructs a new row-oriented map input file from the provided arguments.
ComiFileSource<K,V> - Class in sbrt.shell.io
This class is used to provided a source of column-oriented map input files.
ComiFileSource(Iterator<String>, FileFormat, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.ComiFileSource
Constructs a new source of column-oriented map input files.
ComiFileSource(Iterator<String>, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.ComiFileSource
Constructs a new source of column-oriented map input files.
ComiFileSource(Iterator<String>, FileFormat, MapFormat<K, V>) - Constructor for class sbrt.shell.io.ComiFileSource
Constructs a new source of column-oriented map input files.
COMMA - Static variable in class sbrt.shell.text.SpecialChars
,
ComoFile<K,V> - Class in sbrt.shell.io
This class is used to write maps to text files in a column-oriented way.
ComoFile(String, FileFormat, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.ComoFile
Constructs a new column-oriented map output file from the provided arguments.
ComoFile(String, FileFormat, String, MapFormat<K, V>) - Constructor for class sbrt.shell.io.ComoFile
Constructs a new column-oriented vector output file from the provided arguments.
ComoFile(String, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.ComoFile
Constructs a new text-based column-oriented map output file from the provided arguments.
ComoFileSource<K,V> - Class in sbrt.shell.io
This class is used to provided a source of column-oriented map output files.
ComoFileSource(Iterator<String>, FileFormat, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.ComoFileSource
Constructs a new source of column-oriented map output files.
ComoFileSource(Iterator<String>, FileFormat, String, MapFormat<K, V>) - Constructor for class sbrt.shell.io.ComoFileSource
Constructs a new source of column-oriented map output files.
ComoFileSource(Iterator<String>, FileFormat, MapFormat<K, V>) - Constructor for class sbrt.shell.io.ComoFileSource
Constructs a new source of column-oriented map output files.
complete() - Method in class sbrt.kernel.utilities.PercentProgressMonitor
Sets the internal counter equal to the provided total.
COMPLETED - Static variable in class sbrt.shell.mng.AbstractProcessManager
The prefix used to denote the number of completed operations.
ConflictingInputException - Exception in sbrt.kernel.io
This class is used to indicate conflicting inputs.
ConflictingInputException(List<?>) - Constructor for exception sbrt.kernel.io.ConflictingInputException
Constructs a new conflicting input exception.
CONSTRAINT_TOLERANCE - Static variable in class sbrt.shell.mng.fba.FbaManager
The keyword used to denote a constraint tolerance.
CONSTRAINT_TOLERANCE - Static variable in class sbrt.shell.mng.geom.CdHarManager
The keyword used to denote the constraint tolerance.
CONSTRAINTS_FILE - Static variable in class sbrt.shell.mng.fba.FbaOptManager
The keyword used to denote a constraints file.
ConstraintsFileLineFormat<E> - Interface in sbrt.shell.text.fba
This interface is used to represent formats for flux constraints files.
ConstraintsFileLineFormatV1 - Class in sbrt.shell.text.fba
This class is a concrete implemenation of ConstraintsFileLineFormat.
ConstraintsFileLineFormatV1(Fluxome) - Constructor for class sbrt.shell.text.fba.ConstraintsFileLineFormatV1
Constructs a new contraints file line format.
ConstraintsFileLineFormatV2 - Class in sbrt.shell.text.fba
This class is a concrete implemenation of ConstraintsFileLineFormat.
ConstraintsFileLineFormatV2(Fluxome) - Constructor for class sbrt.shell.text.fba.ConstraintsFileLineFormatV2
Constructs a new contraints file line format.
ConstraintViolationException - Exception in sbrt.kernel.math
This class is used to indicate a constraint violation.
ConstraintViolationException(Object, Interval, double) - Constructor for exception sbrt.kernel.math.ConstraintViolationException
Constructs a new constraint violation exception.
ConstraintViolationException(Object, Interval, Number) - Constructor for exception sbrt.kernel.math.ConstraintViolationException
Constructs a new constraint violation exception.
contains(Object) - Method in class sbrt.kernel.math.graph_theory.Path
Returns true if this path contains the specified node.
contains(Object) - Method in class sbrt.kernel.utilities.LogicalRelation
Indicates if this logical relationship contains the provided condition.
contains(Object) - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.contains(Object).
contains(Object) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.contains(Object).
contains(Object) - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.contains(Object).
containsAll(Collection<?>) - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.containsAll(Collection).
containsAll(Collection<?>) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.containsAll(Collection).
containsAll(Collection<?>) - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.containsAll(Collection).
containsKey(Object) - Method in class sbrt.kernel.utilities.UnmodifiableMap
See Map.containsKey(Object).
containsValue(Object) - Method in class sbrt.kernel.utilities.UnmodifiableMap
See Map.containsValue(Object).
convertConstraints(Map<LinearComb<String>, Interval>, Fluxome, double) - Static method in class sbrt.shell.io.fba.FluxIntervalInputFile
Converts the provided intervals into a FluxConstraints object.
convertVariables(Set<String>) - Static method in class sbrt.shell.io.fba.FluxIntervalInputFile
Converts a set of reaction names to a set of single-term linear combinations.
ConvexPolytope<V> - Interface in sbrt.kernel.math.geom
This interface is used to represent convex polytopes that are represented as the intersection of a finite set of half-spaces.
corr(Map<? extends V, Double>, Map<? extends V, Double>) - Method in class sbrt.ext.R.stat.RCorrelator
Computes and returns the correlation statistic of the provided x and y values.
corr(Double[], Double[]) - Method in class sbrt.ext.R.stat.RCorrelator
Computes and returns the correlation results for the provided values.
corr(Collection<Double>, Collection<Double>) - Method in class sbrt.ext.R.stat.RCorrelator
Computes and returns the correlation results for the provided values.
corr(Map<? extends V, Double>, Map<? extends V, Double>) - Method in interface sbrt.kernel.math.stat.comp.Correlator
Computes and returns the correlation statistic of the provided x and y values.
corr(Collection<Double>, Collection<Double>) - Method in interface sbrt.kernel.math.stat.comp.Correlator
Computes and returns the correlation statistic of the provided x and y values.
corr(Double[], Double[]) - Method in interface sbrt.kernel.math.stat.comp.Correlator
Computes and returns the correlation statistic of the provided x and y values.
corr(Map<? extends V, Double>, Map<? extends V, Double>) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the correlation results for the provided values.
corr(Collection<Double>, Collection<Double>) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the correlation results for the provided values.
corr(Double[], Double[]) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the correlation results for the provided values.
corr(double[], double[]) - Method in class sbrt.kernel.math.stat.comp.KendallTau
Computes and returns the correlation results for the provided values.
CORR_COEFF - Static variable in class sbrt.shell.mng.stat.CorrelationManager
The keyword used to denote the type of correlation coefficient to be computed.
CorrelationAnalysis<V,T extends CorrResult> - Class in sbrt.kernel.math.stat.proc
This class is used to perform correlation processes.
CorrelationAnalysis(Correlator<V, T>) - Constructor for class sbrt.kernel.math.stat.proc.CorrelationAnalysis
Constructs a new correlation process.
CorrelationManager - Class in sbrt.shell.mng.stat
This class is used to manage correlation processes.
CorrelationManager() - Constructor for class sbrt.shell.mng.stat.CorrelationManager
 
Correlator<V,T extends CorrResult> - Interface in sbrt.kernel.math.stat.comp
This interface is used to represent correlation statistic computers.
CorrResFormatterV1 - Class in sbrt.shell.text.math
This class is a concrete implementation of CorrResultsFormatter.
CorrResFormatterV1() - Constructor for class sbrt.shell.text.math.CorrResFormatterV1
Constructs a new correlation results formatter.
CorrResult - Interface in sbrt.kernel.math.stat.comp
This interface is used to represent objects that store the results of a correlation computation.
CorrResultsFormatter<T> - Interface in sbrt.shell.text.math
This interface is used to format the results of a correlation computation.
CPLEX - Static variable in class sbrt.shell.ProgramSolverFactory
The string used to denote the CPLEX program solver from ILOG.
CplexSolver<R,C> - Class in sbrt.ext.cplex
This class is a wrapper for the CPLEX package from ILOG.
CplexSolver() - Constructor for class sbrt.ext.cplex.CplexSolver
Constructs a new CPLEX program solver.
createAndShowWindow() - Method in class sbrt.shell.gui.TextPaneGui
Creates and shows the SBRT's GUI.
CV_FILE - Static variable in class sbrt.shell.mng.fba.IntervalVariationManager
The keyword used to denote a constraint variation input file.
CvCatalystDeletionManager - Class in sbrt.shell.mng.fba
This class is used to manage FBA constraint variation-catalyst deletion processes.
CvCatalystDeletionManager() - Constructor for class sbrt.shell.mng.fba.CvCatalystDeletionManager
 
CvCatalystDeletionProcess<F extends CatalyzedFluxome> - Class in sbrt.kernel.fba.proc
This class is used to perform constraint-variation catalyst deletion processes.
CvCatalystDeletionProcess(RxnDeletionComputer<F>) - Constructor for class sbrt.kernel.fba.proc.CvCatalystDeletionProcess
Constructs a new constraint-variation catalyst deletion process.
CvFbaOptManager - Class in sbrt.shell.mng.fba
This class is used to manage constraint variation-FBA optimization processes.
CvFbaOptManager() - Constructor for class sbrt.shell.mng.fba.CvFbaOptManager
 
CvFbaOptProcess<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to perform constraint-variation FBA optimization processes.
CvFbaOptProcess(FbaOptimizer<F>) - Constructor for class sbrt.kernel.fba.proc.CvFbaOptProcess
Constructs a new constraint-variation FBA optimization process.
CvFluxIntervalProcess<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to perform constraint variation flux interval processes.
CvFluxIntervalProcess(FluxIntervalComputer<F>) - Constructor for class sbrt.kernel.fba.proc.CvFluxIntervalProcess
Constructs a new constraint variation flux interval process.
CvMsFluxIntervalManager - Class in sbrt.shell.mng.fba
This class is used to manage constraint variation-Mahadevan-Schilling flux interval processes.
CvMsFluxIntervalManager() - Constructor for class sbrt.shell.mng.fba.CvMsFluxIntervalManager
 
CvObjectiveFunctionManager - Class in sbrt.shell.mng.fba
This class is used to manage FBA constraint variation-objective function processes.
CvObjectiveFunctionManager() - Constructor for class sbrt.shell.mng.fba.CvObjectiveFunctionManager
 
CvObjectiveFunctionProcess<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to perform constraint-variation objective function processes.
CvObjectiveFunctionProcess(FbaOptimizer<F>) - Constructor for class sbrt.kernel.fba.proc.CvObjectiveFunctionProcess
Constructs a new constraint-variation objective function process.
CvRevRxnFluxIntervalManager - Class in sbrt.shell.mng.fba
This class is used to manage constraint variation-constrained reverse reaction flux interval processes.
CvRevRxnFluxIntervalManager() - Constructor for class sbrt.shell.mng.fba.CvRevRxnFluxIntervalManager
 
CvRxnDeletionManager - Class in sbrt.shell.mng.fba
This class is used to manage FBA constraint variation-reaction deletion processes.
CvRxnDeletionManager() - Constructor for class sbrt.shell.mng.fba.CvRxnDeletionManager
 
CvRxnDeletionProcess<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to perform constraint-variation reaction deletion processes.
CvRxnDeletionProcess(RxnDeletionComputer<F>) - Constructor for class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Constructs a new constraint-variation reaction deletion process.
CvSimpleFluxIntervalManager - Class in sbrt.shell.mng.fba
This class is used to manage constraint variation-simple flux interval processes.
CvSimpleFluxIntervalManager() - Constructor for class sbrt.shell.mng.fba.CvSimpleFluxIntervalManager
 
CYCLE_FILE - Static variable in class sbrt.shell.mng.fba.FluxCapManager
The keyword used to denote the steady state cycle input file.
CycleComputer<F extends Fluxome> - Interface in sbrt.kernel.fba.comp
This interface is used to represent algorithms for identifying steady state cycles in stoichiometric networks.
CycleIdManager - Class in sbrt.shell.mng.graph_theory
This class is used to manage simple cycle identification processes.
CycleIdManager() - Constructor for class sbrt.shell.mng.graph_theory.CycleIdManager
 
CycleIdProcess<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to execute steady state cycle identification processes.
CycleIdProcess(F, CycleComputer<F>) - Constructor for class sbrt.kernel.fba.proc.CycleIdProcess
Constructs a new steady state cycle identification process.
CycleIdProcess<N> - Class in sbrt.kernel.math.graph_theory.proc
This class is used to identify all the simple cycles in a directed graph.
CycleIdProcess() - Constructor for class sbrt.kernel.math.graph_theory.proc.CycleIdProcess
Constructs a new cycle-identification process.

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