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

R

R - Class in sbrt.ext.R
This class is used to access the R engine safely.
RandConstGeneratorV1<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to generate random flux constraints.
RandConstGeneratorV1(F) - Constructor for class sbrt.kernel.fba.proc.RandConstGeneratorV1
Constructs a new random constraint generator.
RandomConstraintsManager - Class in sbrt.shell.mng.fba
This class is used to manage random constraints generators.
RandomConstraintsManager() - Constructor for class sbrt.shell.mng.fba.RandomConstraintsManager
 
RandomFluxVectorManager - Class in sbrt.shell.mng.fba
This abstract class provides a foundation for random flux vector managers.
RandomFluxVectorManager() - Constructor for class sbrt.shell.mng.fba.RandomFluxVectorManager
 
RandomObjectiveGenerator<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to generate random objective functions.
RandomObjectiveGenerator(F) - Constructor for class sbrt.kernel.fba.proc.RandomObjectiveGenerator
Constructs a new random objective function generator.
RandomObjectiveManager - Class in sbrt.shell.mng.fba
This class is used to manage random objective function generators.
RandomObjectiveManager() - Constructor for class sbrt.shell.mng.fba.RandomObjectiveManager
 
rangesEqualZero(Map<?, Interval>, double) - Method in class sbrt.kernel.fba.analysis.FluxIntervalAnalyzer
Returns the number of provided intervals whose ranges equal zero.
rangesEqualZero(Collection<Interval>, double) - Method in class sbrt.kernel.fba.analysis.FluxIntervalAnalyzer
Returns the number of provided intervals whose ranges equal zero.
rangesGreaterThanZero(Map<?, Interval>, double) - Method in class sbrt.kernel.fba.analysis.FluxIntervalAnalyzer
Returns the number of provided intervals whose ranges are greater than zero.
rangesGreaterThanZero(Collection<Interval>, double) - Method in class sbrt.kernel.fba.analysis.FluxIntervalAnalyzer
Returns the number of provided intervals whose ranges are greater than zero.
rBusy(Rengine, int) - Method in class sbrt.ext.R.DummyConsole
Does nothing.
rChooseFile(Rengine, int) - Method in class sbrt.ext.R.DummyConsole
Does nothing.
RCorrelator<V> - Class in sbrt.ext.R.stat
This class computes correlation statistics using R.
RCorrelator() - Constructor for class sbrt.ext.R.stat.RCorrelator
 
RCorrelator.Result - Class in sbrt.ext.R.stat
This class is used to store the results of computing a correlation using R.
RedundRxnRemover - Class in sbrt.kernel.fba.comp
This class is used to remove "redundant" reactions from fluxomes.
RedundRxnRemover() - Constructor for class sbrt.kernel.fba.comp.RedundRxnRemover
 
RedundRxnRemoverManager - Class in sbrt.shell.mng.fba
This class is used to manage redundant reaction remover processes.
RedundRxnRemoverManager() - Constructor for class sbrt.shell.mng.fba.RedundRxnRemoverManager
 
RedundRxnRemoverProcess - Class in sbrt.kernel.fba.proc
This class is used to remove redundant reactions from a fluxome.
RedundRxnRemoverProcess(MixedFluxome) - Constructor for class sbrt.kernel.fba.proc.RedundRxnRemoverProcess
Constructs a new redundant reaction remover process.
RedundRxnRemoverProcess(IrrevRxnFluxome) - Constructor for class sbrt.kernel.fba.proc.RedundRxnRemoverProcess
Constructs a new redundant reaction remover process.
remove(MixedFluxome) - Static method in class sbrt.kernel.fba.comp.RedundRxnRemover
Returns a fluxome for which all "redundant" reactions have been eliminated.
remove(IrrevRxnFluxome) - Static method in class sbrt.kernel.fba.comp.RedundRxnRemover
Returns a fluxome for which all "redundant" reactions have been eliminated.
remove(Object) - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.remove(Object).
remove() - Method in class sbrt.kernel.utilities.UnmodifiableIterator
Throws UnsupportedOperationException.
remove(Object) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.remove(Object).
remove(int) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.remove(int).
remove(Object) - Method in class sbrt.kernel.utilities.UnmodifiableMap
See Map.remove(Object).
remove(Object) - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.remove(Object).
remove() - Method in class sbrt.shell.io.ComiFileSource
Throws UnsupportedOperationException.
remove() - Method in class sbrt.shell.io.ComoFileSource
Throws UnsupportedOperationException.
remove() - Method in class sbrt.shell.io.fba.CofoofSource
Throws UnsupportedOperationException.
remove() - Method in class sbrt.shell.io.fba.RofoofSource
Throws UnsupportedOperationException.
remove() - Method in class sbrt.shell.io.fba.SfoofSource
Throws UnsupportedOperationException.
remove() - Method in class sbrt.shell.io.RomiFileSource
Throws UnsupportedOperationException.
remove() - Method in class sbrt.shell.io.RomoFileSource
Throws UnsupportedOperationException.
remove() - Method in class sbrt.shell.io.SerializedFileIterator
Throws UnsupportedOperationException.
remove() - Method in class sbrt.shell.io.SmoFileSource
Throws UnsupportedOperationException.
remove() - Method in class sbrt.shell.io.TextFileLineIterator
Throws UnsupportedOperationException.
removeAll(Collection<?>) - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.removeAll(Collection).
removeAll(Collection<?>) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.removeAll(Collection).
removeAll(Collection<?>) - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.removeAll(Collection).
removeColumn(Object) - Method in class sbrt.kernel.math.algebra.HashMatrix
Removes the column corresponding to the provided column index.
removeColumn(Object) - Method in interface sbrt.kernel.math.algebra.MatrixBuilder
Removes the column corresponding to the provided column index.
removeColumn(Object) - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Removes the column corresponding to the provided column index.
removeColumn(Object) - Method in class sbrt.kernel.math.algebra.TreeMatrix
Removes the column corresponding to the provided column index.
removeRow(Object) - Method in class sbrt.kernel.math.algebra.HashMatrix
Removes the row corresponding to the provided row index.
removeRow(Object) - Method in interface sbrt.kernel.math.algebra.MatrixBuilder
Removes the row corresponding to the provided row index.
removeRow(Object) - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Removes the row corresponding to the provided row index.
removeRow(Object) - Method in class sbrt.kernel.math.algebra.TreeMatrix
Removes the row corresponding to the provided row index.
replaceConstraints(FluxConstraints, double) - Method in interface sbrt.kernel.fba.CatalyzedFluxome
Returns a copy of this fluxome, but with all constraints replaced by those provided.
replaceConstraints(FluxConstraints, double) - Method in interface sbrt.kernel.fba.Fluxome
Returns a copy of this fluxome, but with all constraints replaced by those provided.
replaceConstraints(FluxConstraints, double) - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Returns a copy of this fluxome, but with all constraints replaced by those provided.
replaceConstraints(FluxConstraints, double) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns a copy of this fluxome, but with all constraints replaced by those provided.
replaceConstraints(FluxConstraints, double) - Method in interface sbrt.kernel.fba.MixedFluxome
Returns a copy of this fluxome, but with all constraints replaced by those provided.
replaceConstraints(FluxConstraints, double) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns a copy of this fluxome, but with all constraints replaced by those provided.
requiredKeywords - Static variable in class plug_in_example.shell.GreetingManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.AbstractProcessManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.algebra.LinearCombConverterManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.algebra.LinearSolverManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.algebra.MatrixConverterManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.algebra.MultipleVectorsConverterManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.algebra.SingleVectorConverterManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.comb.SingleElementUnionManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.comb.StrictSingleElementUnionManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.BiggSbmlReaderManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.CatalystDeletionManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.CdHarFluxVectorManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.CvCatalystDeletionManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.CvFbaOptManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.CvMsFluxIntervalManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.CvObjectiveFunctionManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.CvRevRxnFluxIntervalManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.CvRxnDeletionManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.CvSimpleFluxIntervalManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.ExtremeCurrentManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.FbaManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.FbaOptManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.FbaSolverManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.FluxActivityManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.FluxCapManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.FluxPlasticityManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.InitialPointManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.MetatoolInputReaderManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.MetatoolInputWriterManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.MetatoolOutputReaderManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.MsFluxIntervalManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.MsFluxomeReducerManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.NetworkInfoManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.ObjectiveFunctionManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.PalssonSbmlReaderManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.RandomConstraintsManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.RandomObjectiveManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.RedundRxnRemoverManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.ReverseRxnFluxIntervalManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.RevRxnBreakerManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.RxnDeletionManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.SimpleRxnFileTransManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.SlpCycleIdManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.fba.WwFluxomeReducerManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.geom.CdHarManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.graph_theory.CycleIdManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.graph_theory.GraphInfoManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.graph_theory.PathIdManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.graph_theory.UniqueCycleIdManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.stat.CorrelationManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.stat.KendallTauManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.stat.MannWhitneyUManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.utilities.IntervalComparisonManager
The set of keywords required by this process manager.
requiredKeywords - Static variable in class sbrt.shell.mng.utilities.VariableParticipationManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
requiredKeywords - Static variable in class sbrt.shell.mng.utilities.VectorComparisonManager
The set of keywords required by this process manager.
resetCount() - Method in class sbrt.kernel.utilities.AbstractProgressMonitor
Causes this progress monitor to reset it's internal counter to 0.
resetCount() - Method in interface sbrt.kernel.utilities.MutableProgressMonitor
Causes this progress monitor to reset its internal counter to 0.
resetCount() - Method in class sbrt.kernel.utilities.PercentProgressMonitor
Causes this progress monitor to reset it's internal counter to 0.
restoreColExprConstraint(MathExpr<?>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraint on the provided expression of column variables to the value contained in the fluxome.
restoreColExprConstraints(Collection<? extends MathExpr<?>>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraints for the provided column variable expressions to those in the provided fluxome.
restoreColExprConstraints() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraints on all mathematical expressions of column variables.
restoreColumnConstraint(Object) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraint for the provided column variable to the value contained in the fluxome.
restoreColumnConstraints(Collection<?>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraints for the provided column variables to those in the provided fluxome.
restoreColumnConstraints() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraints on all column variables to those contained in the fluxome used by this optimization computer.
restoreConstraints(FluxConstraints, FluxCvComputer<?>) - Static method in class sbrt.kernel.fba.proc.AbstractCvFbaOptProcess
Restores the provided constraints in the provided constraint-variation computer.
restoreFluxConstraint(String) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Restores the flux constraint for the reaction with the provided name to the value contained in the fluxome.
restoreFluxConstraint(String) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Restores the flux constraint for the reaction with the provided name to the value contained in the fluxome.
restoreFluxConstraint(String) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the flux constraint for the reaction with the provided name to the value contained in the fluxome.
restoreFluxConstraint(String) - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Restores the flux constraint for the reaction with the provided name to the value contained in the fluxome.
restoreFluxConstraint(String) - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Restores the flux constraint for the reaction with the provided name to the value contained in the fluxome.
restoreFluxConstraint(String) - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Restores the flux constraint for the reaction with the provided name to the value contained in the fluxome.
restoreFluxConstraints(Collection<String>) - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Restores the flux constraints for the provided reaction names to the values contained in the fluxome.
restoreFluxConstraints() - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Restores the flux constraints for all reactions in the fluxome to those values contained in the fluxome.
restoreFluxConstraints(Collection<String>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Restores the flux constraints for the provided reaction names to the values contained in the fluxome.
restoreFluxConstraints() - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Restores the flux constraints for all reactions in the fluxome to those values contained in the fluxome.
restoreFluxConstraints(Collection<String>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraints for the provided reaction names to those in the provided fluxome.
restoreFluxConstraints() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the flux constraints for all reactions to those contained in the fluxome used by this optimization computer.
restoreFluxConstraints() - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Restores the flux constraints for all reactions in the fluxome to those values contained in the fluxome.
restoreFluxConstraints(Collection<String>) - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Restores the flux constraints for the provided reaction names to the values contained in the fluxome.
restoreFluxConstraints(Collection<String>) - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Restores the flux constraints for the provided reaction names to the values contained in the fluxome.
restoreFluxConstraints() - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Restores the flux constraints for all reactions in the fluxome to those values contained in the fluxome.
restoreMatrixElements() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the program matrix to the stoichiometry matrix of the fluxome used by this computer.
restoreRowConstraint(Object) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraint on the provided row variable.
restoreRowConstraints(Collection<?>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraints for the provided row variables to those in the provided fluxome.
restoreRowConstraints() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraints on all row variables to those contained in the fluxome used by this optimization computer.
restoreRxnExprConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Restores the constraint on the provided flux expression to the value contained in the fluxome.
restoreRxnExprConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Restores the constraint on the provided flux expression to the value contained in the fluxome.
restoreRxnExprConstraint(LinearComb<String>) - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Restores the constraint on the provided flux expression to the value contained in the fluxome.
restoreRxnExprConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraint on the provided flux expression to the value contained in the fluxome.
restoreRxnExprConstraint(MathExpr<String>) - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Restores the constraint on the provided flux expression to the value contained in the fluxome.
restoreRxnExprConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Restores the constraint on the provided flux expression to the value contained in the fluxome.
restoreRxnExprConstraint(MathExpr<String>) - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Restores the constraint on the provided flux expression to the value contained in the fluxome.
restoreRxnExprConstraints(Collection<? extends MathExpr<String>>) - Method in class sbrt.kernel.fba.comp.AbstractCvComputer
Restores the constraints on the provided expressions to the values contained in the fluxome.
restoreRxnExprConstraints(Collection<? extends MathExpr<String>>) - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Restores the constraints on the provided expressions to the values contained in the fluxome.
restoreRxnExprConstraints() - Method in class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Restores the constraints on all flux expressions to the values contained in the fluxome.
restoreRxnExprConstraints() - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Restores the constraints on all flux expressions to the values contained in the fluxome.
restoreRxnExprConstraints(Collection<? extends MathExpr<String>>) - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraints for the provided reaction name expressions to those in the provided fluxome.
restoreRxnExprConstraints() - Method in class sbrt.kernel.fba.comp.FbaOptimizer
Restores the constraints on all mathematical expressions of reaction names.
restoreRxnExprConstraints() - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Restores the constraints on all flux expressions to the values contained in the fluxome.
restoreRxnExprConstraints(Collection<? extends MathExpr<String>>) - Method in interface sbrt.kernel.fba.comp.FluxCvComputer
Restores the constraints on the provided expressions to the values contained in the fluxome.
restoreRxnExprConstraints(Collection<? extends MathExpr<String>>) - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Restores the constraints on the provided expressions to the values contained in the fluxome.
restoreRxnExprConstraints() - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Restores the constraints on all flux expressions to the values contained in the fluxome.
restoreRxnExprConstraints() - Method in class sbrt.kernel.fba.comp.RxnDeletionComputer
Restores the constraints on all flux expressions to the values contained in the fluxome.
ResultsManager<T> - Interface in sbrt.kernel.io
This interace is used to represent a results-manager.
retainAll(Collection<?>) - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.retainAll(Collection).
retainAll(Collection<?>) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.retainAll(Collection).
retainAll(Collection<?>) - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.retainAll(Collection).
REV - Static variable in class sbrt.kernel.fba.MixedFluxomeV1
The constraint used by default for reversible internal reactions: (-Infinity, Infinity).
REV_CONSTRAINT - Static variable in class sbrt.shell.mng.fba.RandomConstraintsManager
The keyword used to denote the constraint for reversible reactions.
REVERSE_SUFFIX - Static variable in class sbrt.kernel.fba.proc.RevRxnBreakerProcess
The default suffix added to the names or IDs of reverse reactions.
reverseChemRxns(ChemRxn, ChemRxn) - Static method in class sbrt.kernel.fba.RxnComparer
Indicates if the provided chemical reactions are the reverse of each other.
reverseExchangeRxns(SourceRxn, SinkRxn) - Static method in class sbrt.kernel.fba.RxnComparer
Indicates if the provided exchange reactions are the reverse of each other.
reverseExchangeRxns(SinkRxn, SourceRxn) - Static method in class sbrt.kernel.fba.RxnComparer
Indicates if the provided exchange reactions are the reverse of each other.
reverseIrrevRxns(IrrevRxn, IrrevRxn) - Static method in class sbrt.kernel.fba.RxnComparer
Indicates if the provided chemical reactions are the reverse of each other.
ReverseRxnFluxIntervalManager - Class in sbrt.shell.mng.fba
This class is used to manage constrained-reverse reaction flux interval processes.
ReverseRxnFluxIntervalManager() - Constructor for class sbrt.shell.mng.fba.ReverseRxnFluxIntervalManager
 
ReverseRxnIntervalComp<F extends IrrevRxnFluxome> - Class in sbrt.kernel.fba.comp
This class is used to compute flux intervals while constraining the fluxes of reverse reactions to their minimum.
ReverseRxnIntervalComp(FbaOptimizer<F>, double) - Constructor for class sbrt.kernel.fba.comp.ReverseRxnIntervalComp
Constructs a new flux interval computer.
RevExchRxn - Class in sbrt.kernel.fba
This class is used to represent reversible exchange reactions, that is, exchange reactions that can both supply and consume chemical species to and from a chemical system.
RevExchRxn(String, boolean) - Constructor for class sbrt.kernel.fba.RevExchRxn
Constructs a new reversible exchange reaction for the provided chemical species.
REVISION - Static variable in class sbrt.Sbrt
Indicates the revision number of the Systems Biology Research Tool.
RevRxn - Class in sbrt.kernel.fba
This class is used to represent reversible chemical reactions.
RevRxn(LinearComb<String>, LinearComb<String>) - Constructor for class sbrt.kernel.fba.RevRxn
Constructs a new reversible reaction from the provided reactants and products.
RevRxnBreakerManager - Class in sbrt.shell.mng.fba
This class is used to manage reversible reaction breakers.
RevRxnBreakerManager() - Constructor for class sbrt.shell.mng.fba.RevRxnBreakerManager
 
RevRxnBreakerProcess - Class in sbrt.kernel.fba.proc
This class is used to break reversible reactions into pairs of irreversible reactions.
RevRxnBreakerProcess() - Constructor for class sbrt.kernel.fba.proc.RevRxnBreakerProcess
Constructs a new reversible reaction breaker process.
RevRxnFormatV1 - Class in sbrt.shell.text.chem
This class is used to format reversible chemical reactions.
RevRxnFormatV1() - Constructor for class sbrt.shell.text.chem.RevRxnFormatV1
Constructs a new reversible reaction format.
RevRxnFormatV1 - Class in sbrt.shell.text.fba
This class is used to format reversible reactions for use in flux balance analysis.
RevRxnFormatV1() - Constructor for class sbrt.shell.text.fba.RevRxnFormatV1
Constructs a new reversible reaction format.
RevRxnFormatV2 - Class in sbrt.shell.text.fba
This class is used to format reversible reactions for use in flux balance analysis.
RevRxnFormatV2() - Constructor for class sbrt.shell.text.fba.RevRxnFormatV2
Constructs a new reversible reaction format.
rFlushConsole(Rengine) - Method in class sbrt.ext.R.DummyConsole
Does nothing.
RIGHT_BRACE - Static variable in class sbrt.shell.text.SpecialChars
{
RIGHT_BRACKET - Static variable in class sbrt.shell.text.SpecialChars
]
RIGHT_PAREN - Static variable in class sbrt.shell.text.SpecialChars
)
rigid() - Method in class sbrt.kernel.fba.proc.FluxPlasticityProcess.Results
Returns the number of rigid fluxes.
RKendall<V> - Class in sbrt.ext.R.stat
This class computes Kendall tau values using R.
RKendall() - Constructor for class sbrt.ext.R.stat.RKendall
 
rLoadHistory(Rengine, String) - Method in class sbrt.ext.R.DummyConsole
Does nothing.
RofoofSource<F extends Fluxome> - Class in sbrt.shell.io.fba
This class is used to provide a source of row-oriented FBA optimization output files.
RofoofSource(Iterator<String>, FileFormat, Set<String>, FbaOptFileLineFormat) - Constructor for class sbrt.shell.io.fba.RofoofSource
Constructs a new source of row-oriented FBA optimization output files.
RofoofSource(Iterator<String>, String, FileFormat, Set<String>, FbaOptFileLineFormat) - Constructor for class sbrt.shell.io.fba.RofoofSource
Constructs a new source of row-oriented FBA optimization output files.
RomiFile<K,V> - Class in sbrt.shell.io
This class is used to read row-oriented map input files.
RomiFile(String, FileFormat, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomiFile
Constructs a new row-oriented map input file from the provided arguments.
RomiFile(String, FileFormat, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomiFile
Constructs a new row-oriented map input file from the provided arguments.
RomiFile(String, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomiFile
Constructs a new row-oriented map input file from the provided arguments.
RomiFile(String, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomiFile
Constructs a new row-oriented map input file from the provided arguments.
RomiFileSource<K,V> - Class in sbrt.shell.io
This class is used to provided a source of row-oriented map input files.
RomiFileSource(Iterator<String>, FileFormat, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomiFileSource
Constructs a new source of row-oriented map input files.
RomiFileSource(Iterator<String>, FileFormat, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomiFileSource
Constructs a new source of row-oriented map input files.
RomiFileSource(Iterator<String>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomiFileSource
Constructs a new source of row-oriented map input files.
RomoFile<K,V> - Class in sbrt.shell.io
This class is used to write maps to text files in a row-oriented way.
RomoFile(String, FileFormat, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomoFile
Constructs a new row-oriented map output file from the provided arguments.
RomoFile(String, FileFormat, String, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomoFile
Constructs a new row-oriented vector output file from the provided arguments.
RomoFile(String, FileFormat, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomoFile
Constructs a new row-oriented vector output file from the provided arguments.
RomoFile(String, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomoFile
Constructs a new plain text, row-oriented vector output file from the provided arguments.
RomoFileSource<K,V> - Class in sbrt.shell.io
This class is used to provided a source of row-oriented map output files.
RomoFileSource(Iterator<String>, FileFormat, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomoFileSource
Constructs a new source of row-oriented map output files.
RomoFileSource(Iterator<String>, FileFormat, String, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomoFileSource
Constructs a new source of row-oriented map output files.
RomoFileSource(Iterator<String>, FileFormat, MapFormat<K, V>) - Constructor for class sbrt.shell.io.RomoFileSource
Constructs a new source of row-oriented map output files.
RowOrFbaOptOutputFile<F extends Fluxome> - Class in sbrt.shell.io.fba
This class is used to write row-oriented output files containing FBA optimization data.
RowOrFbaOptOutputFile(String, FileFormat, Set<String>, FbaOptFileLineFormat) - Constructor for class sbrt.shell.io.fba.RowOrFbaOptOutputFile
Constructs a new row-oriented FBA optimization output file.
RowOrFbaOptOutputFile(String, FileFormat, FbaOptFileLineFormat) - Constructor for class sbrt.shell.io.fba.RowOrFbaOptOutputFile
Constructs a new row-oriented FBA optimization output file.
RowOrTreeMatrix<R extends java.lang.Comparable<? super R>,C extends java.lang.Comparable<? super C>> - Class in sbrt.kernel.math.algebra
This class is a java.util.TreeMap based implementation of SmdMatrix.
RowOrTreeMatrix() - Constructor for class sbrt.kernel.math.algebra.RowOrTreeMatrix
Constructs an emtpy RowOrTreeMatrix.
rows() - Method in class sbrt.kernel.math.algebra.HashMatrix
Returns the number of rows in this matrix.
rows() - Method in interface sbrt.kernel.math.algebra.Matrix
Returns the number of rows in this matrix.
rows() - Method in class sbrt.kernel.math.algebra.MatrixWrap
Returns the number of rows in this matrix.
rows() - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Returns the number of rows in this matrix.
rows() - Method in class sbrt.kernel.math.algebra.TreeMatrix
Returns the number of rows in this matrix.
RPearson<V> - Class in sbrt.ext.R.stat
This class computes Pearson r values using R.
RPearson() - Constructor for class sbrt.ext.R.stat.RPearson
 
rReadConsole(Rengine, String, int) - Method in class sbrt.ext.R.DummyConsole
Does nothing.
rSaveHistory(Rengine, String) - Method in class sbrt.ext.R.DummyConsole
Does nothing.
rShowMessage(Rengine, String) - Method in class sbrt.ext.R.DummyConsole
Does nothing.
RSpearman<V> - Class in sbrt.ext.R.stat
This class computes Spearman rho values using R.
RSpearman() - Constructor for class sbrt.ext.R.stat.RSpearman
 
run(ResultsManager<String>) - Method in class plug_in_example.kernel.GreetingProcess
Adds a randomly generated greeting to the provided results manager.
run() - Method in class sbrt.kernel.fba.comp.CdHarFluxComp
Computes the next random flux vector from within the interior of the convex polytope defined by the current set of constraints.
run() - Method in class sbrt.kernel.fba.comp.InitialPointComputer
Computes an initial point, or flux vector, in the flux space of the fluxome used by this computer.
run(ResultsManager<FbaOptimizer<F>.Results>) - Method in class sbrt.kernel.fba.proc.CatalystDeletionProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<CdHarFluxComp<F>.Results>) - Method in class sbrt.kernel.fba.proc.CdHarFluxVectorProcess
Generates the specified number of random flux vectors and adds each to the provided results manager.
run(ResultsManager<FbaOptimizer<F>.Results>) - Method in class sbrt.kernel.fba.proc.CvCatalystDeletionProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<FbaOptimizer<F>.Results>) - Method in class sbrt.kernel.fba.proc.CvFbaOptProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<Map<String, Interval>>) - Method in class sbrt.kernel.fba.proc.CvFluxIntervalProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<FbaOptimizer<F>.Results>) - Method in class sbrt.kernel.fba.proc.CvObjectiveFunctionProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<FbaOptimizer<F>.Results>) - Method in class sbrt.kernel.fba.proc.CvRxnDeletionProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<DoubleMatrix<?, String>>) - Method in class sbrt.kernel.fba.proc.CycleIdProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<DoubleMatrix<?, String>>) - Method in class sbrt.kernel.fba.proc.ExtremeCurrentProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<FbaOptimizer<F>.Results>) - Method in class sbrt.kernel.fba.proc.FbaOptProcess
Computes the optimal value of the current objective function and adds the results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<LinearSystemSolution<String>>) - Method in class sbrt.kernel.fba.proc.FbaSolverProcess
Solves Sv = 0 and adds the result to the provided manager.
run(ResultsManager<FluxActivityProcess.Results>) - Method in class sbrt.kernel.fba.proc.FluxActivityProcess
Iterates thru the flux vector source set via setFluxVectorSource(Iterable), counts the number of active and inactive fluxes in each vector, and adds the results of each to the provided results manager.
run(ResultsManager<Map<String, Set<LinearComb<String>>>>) - Method in class sbrt.kernel.fba.proc.FluxCapProcess
Computes the flux caps and adds the result to the provided manager.
run(ResultsManager<Map<String, Interval>>) - Method in class sbrt.kernel.fba.proc.FluxIntervalProcess
Computes the flux intervals of the reactions with the current names and adds them to the provided results manager.
run(ResultsManager<T>) - Method in class sbrt.kernel.fba.proc.FluxomeReducerProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<FluxPlasticityProcess.Results>) - Method in class sbrt.kernel.fba.proc.FluxPlasticityProcess
Iterates thru the flux interval source set via setFluxRangeSource(Iterable), computes the flux plasticity measures, and adds the results of each to the provided results manager.
run(ResultsManager<InitialPointComputer<F>.Results>) - Method in class sbrt.kernel.fba.proc.InitialPointGenerator
Generates an initial point and adds it to the provided results manager.
run(ResultsManager<NetworkInfoProcess.Results<F>>) - Method in class sbrt.kernel.fba.proc.NetworkInfoProcess
Adds the information gathered about the fluxome to the provided results manager.
run(ResultsManager<FbaOptimizer<F>.Results>) - Method in class sbrt.kernel.fba.proc.ObjFunAnalysis
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<Map<String, Interval>>) - Method in class sbrt.kernel.fba.proc.RandConstGeneratorV1
Generates sets of random flux constraints and adds them to the provided results manager.
run(ResultsManager<LinearComb<String>>) - Method in class sbrt.kernel.fba.proc.RandomObjectiveGenerator
Generates random objective functions and adds them to the provided results manager.
run(ResultsManager<Fluxome>) - Method in class sbrt.kernel.fba.proc.RedundRxnRemoverProcess
Adds the information gathered about the fluxome to the provided results manager.
run(ResultsManager<Map<String, ChemRxn>>) - Method in class sbrt.kernel.fba.proc.RevRxnBreakerProcess
Breaks the reversible reactions supplied to this process and adds the result to the provided manager.
run(ResultsManager<FbaOptimizer<F>.Results>) - Method in class sbrt.kernel.fba.proc.RxnDeletionProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<CdHarFluxComp<F>.Results>) - Method in class sbrt.kernel.fba.proc.SvCdHarFluxVectorProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<InitialPointComputer<F>.Results>) - Method in class sbrt.kernel.fba.proc.SvInitialPointProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<T>) - Method in interface sbrt.kernel.KernelProcess
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method.
run(ResultsManager<LinearSystemSolution<V>>) - Method in class sbrt.kernel.math.algebra.proc.LinearSolverProcess
Solves the system of linear equations and adds the solution to the provided results manager.
run(ResultsManager<Map<K, V>>) - Method in class sbrt.kernel.math.algebra.proc.VectorIntersection
and adds the results to the provided results manager.
run(ResultsManager<Set<Set<E>>>) - Method in class sbrt.kernel.math.comb.proc.SingleElementUnionProc
Computes the single-element unions of the provided collection of sets, and adds the results to the provided results manager.
run(ResultsManager<Set<Set<E>>>) - Method in class sbrt.kernel.math.comb.proc.StrictSingleElementUnionProc
Computes the strict single-element unions of the provided collection of sets, and adds the results to the provided results manager.
run(Map<? extends V, Double>) - Method in class sbrt.kernel.math.geom.comp.CdHarComp
Computes and returns a random interior point of the convex polytope starting from the provided point.
run(ResultsManager<CdHarComp<V>.Results>) - Method in class sbrt.kernel.math.geom.proc.CdHarProcess
Adds random points to the provided results manager.
run(ResultsManager<Path<N>>) - Method in class sbrt.kernel.math.graph_theory.proc.CycleIdProcess
Adds to the provided results manager each identified cycle in the current graph.
run(ResultsManager<Path<N>>) - Method in class sbrt.kernel.math.graph_theory.proc.PathIdProcess
Adds to the provided results manager each computed path in the current graph.
run(ResultsManager<T>) - Method in class sbrt.kernel.math.stat.proc.CorrelationAnalysis
Computes the correlation statistic between the x and y values, and adds the results to the provided results manager.
run(ResultsManager<T>) - Method in class sbrt.kernel.math.stat.proc.MultipleCorrelationAnalysis
Computes the correlation statistic between the x and y values, and adds the results to the provided results manager.
run(ResultsManager<MannWhitneyResults>) - Method in class sbrt.kernel.math.stat.proc.MwUAnalysis
Computes the Mann-Whitney U statistic of the samples A and B, and adds the results to the provided results manager.
run(ResultsManager<Set<IntervalComparer.Diff<V>>>) - Method in class sbrt.kernel.utilities.proc.IntervalComparison
Adds to the provided results manager the variables (keys) whose intervals (values) are not considered equivalent.
run(ResultsManager<Map<V, List<E>>>) - Method in class sbrt.kernel.utilities.proc.VariableParticipation
Adds to the provided results manager a map of variables mapped to a list of mathematical expressions in which they participate.
run(ResultsManager<Map<V, Double>>) - Method in class sbrt.kernel.utilities.proc.VectorComparison
Adds to the provided results manager the variables (keys) whose intervals (values) are unequal within the provided tolerance.
run(String, PrintWriter) - Method in class sbrt.ProcessRunner
Executes the process specified in the indicated process file.
run(String, OutputStream) - Method in class sbrt.ProcessRunner
Executes the process specified in the indicated process file.
run(String, PrintStream) - Method in class sbrt.ProcessRunner
Executes the process specified in the indicated process file.
run(ManagerInput<String, String>, OutputStream) - Method in class sbrt.ProcessRunner
Executes the process specified in the provided process manager input.
run(ManagerInput<String, String>, PrintStream) - Method in class sbrt.ProcessRunner
Executes the process specified in the provided process manager input.
run(ManagerInput<String, String>, PrintWriter) - Method in class sbrt.ProcessRunner
Executes the process specified in the provided process manager input.
runProcess(MonitoredProcess<T>, ResultsManager<T>, PrintWriter) - Static method in class sbrt.shell.mng.AbstractProcessManager
Runs the provided process using the provided results manager and prints descriptive progress messages to the provided print writer.
rWriteConsole(Rengine, String, int) - Method in class sbrt.ext.R.DummyConsole
Does nothing.
RXN_CATALYST_FILE - Static variable in class sbrt.shell.mng.fba.FbaManager
The keyword used to denote the name of a file containing reaction-catalyst associations.
RXN_DELETION_FILE - Static variable in class sbrt.shell.mng.fba.RxnDeletionManager
The keyword used to denote the name of a file containing sets of names of reactions whose effect upon deletion will be computed.
RXN_FILE - Static variable in class sbrt.shell.mng.fba.FbaManager
The keyword used to denote an FBA reaction file.
RXN_FILE_NAME - Static variable in class sbrt.shell.mng.fba.BiggSbmlReaderManager
Used to denote the name of the file to which chemical reactions should be written.
RXN_FILE_NAME - Static variable in class sbrt.shell.mng.fba.PalssonSbmlReaderManager
Used to denote the name of the file to which chemical reactions should be written.
RXN_NAME_FILE_NAME - Static variable in class sbrt.shell.mng.fba.NetworkInfoManager
The keyword used to denote the name of the file to which the names of reactions of a fluxome will be written.
RXN_NODE_NAME - Static variable in class sbrt.shell.text.fba.BiggRxnNodeParser
The name of the nodes parsed by this class ('reaction').
RXN_NODE_NAME - Static variable in class sbrt.shell.text.fba.PalssonRxnNodeParser
The name of the nodes parsed by this class ('reaction').
RXN_OUTPUT_FILE_NAME - Static variable in class sbrt.shell.mng.fba.NetworkInfoManager
The keyword used to denote the name of the file to which a fluxome will be written.
RxnComparer - Class in sbrt.kernel.fba
This class is used to compare chemical reactions.
RxnComparer() - Constructor for class sbrt.kernel.fba.RxnComparer
 
RxnDeletionComputer<F extends Fluxome> - Class in sbrt.kernel.fba.comp
This class is used to compute the effect of deleting reactions in a fluxome.
RxnDeletionComputer(FbaOptimizer<F>) - Constructor for class sbrt.kernel.fba.comp.RxnDeletionComputer
Constructs a new reaction deletion computer.
RxnDeletionManager - Class in sbrt.shell.mng.fba
This class is used to manage FBA reaction deletion processes.
RxnDeletionManager() - Constructor for class sbrt.shell.mng.fba.RxnDeletionManager
 
RxnDeletionProcess<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to perform reaction deletion processes.
RxnDeletionProcess(RxnDeletionComputer<F>) - Constructor for class sbrt.kernel.fba.proc.RxnDeletionProcess
Constructs a new reaction deletion process.
RxnFormatV1 - Class in sbrt.shell.text.fba
This class is used to format reactions for use in flux balance analysis.
RxnFormatV1() - Constructor for class sbrt.shell.text.fba.RxnFormatV1
Constructs a new irreversible reaction format.
RxnNameExprFormat<E extends MathExpr<S>,S> - Interface in sbrt.shell.text.fba
This interface is used to represent formats for mathematical expressions of reaction names.
RxnNameExprFormatV1 - Class in sbrt.shell.text.fba
This class is used to format linear combinations of reaction names.
RxnNameExprFormatV1(Fluxome) - Constructor for class sbrt.shell.text.fba.RxnNameExprFormatV1
Constructs a new reaction name expression format using the provided fluxome.
RxnNameExprFormatV1(Fluxome, double) - Constructor for class sbrt.shell.text.fba.RxnNameExprFormatV1
Constructs a new reaction name expression format using the provided fluxome.
RxnNameFormat<T> - Interface in sbrt.shell.text.chem
This interface is used to represent formats for the names of chemical reactions.
RxnNameFormatV1 - Class in sbrt.shell.text.chem
This class is a concrete implementation of RxnNameFormat.
RxnNameFormatV1() - Constructor for class sbrt.shell.text.chem.RxnNameFormatV1
 
RxnNameListFormat - Interface in sbrt.shell.text.fba
This interface is used to represent the formats of collections of reaction names.
RxnNameListFormatV1 - Class in sbrt.shell.text.fba
This class is a concrete implemenation of RxnNameListFormat.
RxnNameListFormatV1(Fluxome) - Constructor for class sbrt.shell.text.fba.RxnNameListFormatV1
Constructs a new reaction name list format using the provided fluxome.
RxnNameOrExprFormat - Interface in sbrt.shell.text.fba
This interface is used to represent formats for reaction names and mathematical expressions of reaction names.
RxnNameOrExprFormatV1 - Class in sbrt.shell.text.fba
This class is a concrete implemenation of RxnNameOrExprFormat.
RxnNameOrExprFormatV1(Fluxome) - Constructor for class sbrt.shell.text.fba.RxnNameOrExprFormatV1
Constructs a new reaction name and expression format.
RxnNameSetFormat - Interface in sbrt.shell.text.fba
This interface is used to represent the formats of collections of reaction names.
RxnNameSetFormatV1 - Class in sbrt.shell.text.fba
This class is a concrete implemenation of RxnNameSetFormat.
RxnNameSetFormatV1(Fluxome) - Constructor for class sbrt.shell.text.fba.RxnNameSetFormatV1
Constructs a new reaction name collection format using the provided fluxome.
RxnNameVerifier - Class in sbrt.shell.text.fba
This class is used to ensure reaction names exist in a given Fluxome.
RxnNameVerifier(Fluxome) - Constructor for class sbrt.shell.text.fba.RxnNameVerifier
Constructs a new reaction name checker for the provided fluxome.
RxnNamExprSetInputFile<E extends MathExpr<S>,S> - Class in sbrt.shell.io.fba
This class is used to read files containing a set of reaction name expressions.
RxnNamExprSetInputFile(String, RxnNameExprFormat<E, S>) - Constructor for class sbrt.shell.io.fba.RxnNamExprSetInputFile
Constructs a new reaction name expression set input file.
rxns() - Method in interface sbrt.kernel.fba.Fluxome
Returns the total number of chemical reactions contained in this fluxome.
rxns() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the total number of chemical reactions contained in this fluxome.
rxns() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the total number of chemical reactions contained in this fluxome.

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