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

I

IllegalBoundsException - Exception in sbrt.kernel.math
This class is used to indicate the existence of illegal bounds.
IllegalBoundsException(Number, Number) - Constructor for exception sbrt.kernel.math.IllegalBoundsException
Constructs a new illegal bounds exception from the provided lower and upper bounds.
IllegalBoundsException(double, double) - Constructor for exception sbrt.kernel.math.IllegalBoundsException
Constructs a new illegal bounds exception from the provided lower and upper bounds.
IllegalBoundsException(Object, double, double) - Constructor for exception sbrt.kernel.math.IllegalBoundsException
Constructs a new illegal bounds exception from the provided lower and upper bounds.
IllegalBoundsException(Object, Number, Number) - Constructor for exception sbrt.kernel.math.IllegalBoundsException
Constructs a new illegal bounds exception from the provided lower and upper bounds.
IllegalFreeVariableException - Exception in sbrt.kernel.math.algebra
This class is used to indicate the presence of an illegal free variable.
IllegalFreeVariableException(Object) - Constructor for exception sbrt.kernel.math.algebra.IllegalFreeVariableException
Constructs a new illegal free variable exception.
inactive() - Method in class sbrt.kernel.fba.proc.FluxActivityProcess.Results
Returns the number of inactive fluxes.
INACTIVE - Static variable in class sbrt.shell.mng.fba.RandomConstraintsManager
The keyword used to denote the inactive constraint.
increment() - Method in class sbrt.kernel.utilities.AbstractProgressMonitor
Causes this progress monitor to increment an internal counter.
increment() - Method in interface sbrt.kernel.utilities.MutableProgressMonitor
Causes this progress monitor to increment an internal counter.
increment() - Method in class sbrt.kernel.utilities.PercentProgressMonitor
Causes this progress monitor to increment an internal counter.
indexOf(Object) - Method in class sbrt.kernel.math.graph_theory.Path
Returns the index in this path of the first occurrence of the specified node, or -1 if this path does not contain that node.
indexOf(Object) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.indexOf(Object).
IndexPair<R,C> - Class in sbrt.kernel.math.algebra
This class is used to represent pairs of matrix indices.
IndexPair(S, T) - Constructor for class sbrt.kernel.math.algebra.IndexPair
Constructs a new pair of matrix indices.
IndexPairFormat<R,C> - Interface in sbrt.shell.text.math
This interface is used to represent formats for pairs of indices.
IndexPairFormatV1<R,C> - Class in sbrt.shell.text.math
This class is a concrete implementation of IndexPairFormat.
IndexPairFormatV1(SimpleFormat<R>, SimpleFormat<C>) - Constructor for class sbrt.shell.text.math.IndexPairFormatV1
Constructs a new index pair format.
InfeasibleSolutionException - Exception in sbrt.kernel.math
This class is used to indicate that no feasible solution exists.
InfeasibleSolutionException(Object) - Constructor for exception sbrt.kernel.math.InfeasibleSolutionException
Constructs a new infeasible solution exception.
InfeasibleSolutionException(Object, String) - Constructor for exception sbrt.kernel.math.InfeasibleSolutionException
Constructs a new infeasible solution exception.
InfeasibleSolutionException(Object, Throwable) - Constructor for exception sbrt.kernel.math.InfeasibleSolutionException
Constructs a new infeasible solution exception.
InfeasibleSolutionException(Object, String, Throwable) - Constructor for exception sbrt.kernel.math.InfeasibleSolutionException
Constructs a new infeasible solution exception.
INITIAL_POINT_FILE - Static variable in class sbrt.shell.mng.geom.CdHarManager
The keyword used to denote the initial point file.
InitialPointComputer<F extends Fluxome> - Class in sbrt.kernel.fba.comp
This class is used to compute initial points for coordinate-direction hit-and-run random flux vector algorithms.
InitialPointComputer(FbaOptimizer<F>) - Constructor for class sbrt.kernel.fba.comp.InitialPointComputer
Constructs a new initial point, or flux vector, computer.
InitialPointComputer.Results - Class in sbrt.kernel.fba.comp
This class is used to represent the results of the initial point computation.
InitialPointGenerator<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to execute initial point generators.
InitialPointGenerator(InitialPointComputer<F>) - Constructor for class sbrt.kernel.fba.proc.InitialPointGenerator
Constructs a new initial point process.
InitialPointManager - Class in sbrt.shell.mng.fba
This class is used to manage initial point processes.
InitialPointManager() - Constructor for class sbrt.shell.mng.fba.InitialPointManager
 
INPUT_FILE - Static variable in class sbrt.shell.mng.AbstractProcessManager
The keyword used to denote the name of the input file.
INPUT_FILE_FORMAT - Static variable in class sbrt.shell.mng.AbstractProcessManager
The keyword used to denote the name of an input file format.
INPUT_FILE_NAME_FILE - Static variable in class sbrt.shell.mng.AbstractProcessManager
The keyword used to denote the name of a file containing a list of file names.
INPUT_RXN_FILE - Static variable in class sbrt.shell.mng.fba.SimpleRxnFileTransManager
The keyword used to denote the name of the input reaction file.
InputFile<E> - Interface in sbrt.shell.io
This interface is used to represent input files.
IntegerFormat - Interface in sbrt.shell.text
This interface is used to represent a format for integers.
IntegerFormatV1 - Class in sbrt.shell.text
This class is a concrete implementation of IntegerFormat.
IntegerFormatV1() - Constructor for class sbrt.shell.text.IntegerFormatV1
 
internalRxns() - Method in interface sbrt.kernel.fba.Fluxome
Returns the total number of internal reactions contained in this fluxome.
internalRxns() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the total number of internal reactions contained in this fluxome.
internalRxns() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the total number of internal reactions contained in this fluxome.
interpret(Throwable) - Static method in class sbrt.ProcessRunner
Interprets the provided throwable.
interpret(ExternalSoftwareException) - Static method in class sbrt.shell.mng.algebra.LinearSolverManager
Interprets the provided external software exception.
interpret(RuntimeException) - Static method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Attempts to interpret the provided RuntimeException.
interpret(DimensionException) - Static method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(InfeasibleSolutionException) - Static method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(UnboundedVariableException) - Static method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(InvalidFluxVectorException) - Static method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(ExceededLimitException) - Static method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(ConflictingInputException, String, String) - Static method in class sbrt.shell.mng.fba.CvRxnDeletionManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(RuntimeException, FbaProcess<?, ?>) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(ProgramSolverException) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(ConstraintViolationException, FbaProcess<?, ?>) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(FbaOptException, FbaProcess<?, ?>) - Static method in class sbrt.shell.mng.fba.FbaOptManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(FbaOptException, FbaProcess<?, ?>) - Static method in class sbrt.shell.mng.fba.InitialPointManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(FluxRangeException, FbaProcess<?, ?>) - Static method in class sbrt.shell.mng.fba.MsFluxIntervalManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(IllegalBoundsException) - Static method in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(UnboundedVariableException) - Static method in class sbrt.shell.mng.geom.CdHarManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(ExceededLimitException) - Static method in class sbrt.shell.mng.geom.CdHarManager
Returns an ApplicationException whose message describes the error that ocurred.
interpret(JriException) - Static method in class sbrt.shell.mng.stat.CorrelationManager
Wraps the provided JRI exception as an application exception.
interpret(ProgramSolverException) - Static method in class sbrt.shell.ProgramSolverFactory
Interprets a program solver exception and returns a corresponding application exception.
interpretSolution(Expr) - Static method in class sbrt.ext.mma.algebra.MMaExprInterpretter
Converts the provided Mathematica expression to a Map.
Interval - Class in sbrt.kernel.math
This class is used to represent closed intervals of the form [α, &beta], where α ≤ β.
Interval(double, double) - Constructor for class sbrt.kernel.math.Interval
Constructs a new interval with the provided lower and upper bounds.
IntervalComparer - Class in sbrt.kernel.math
This class is used to compare vectors of intervals.
IntervalComparer() - Constructor for class sbrt.kernel.math.IntervalComparer
 
IntervalComparer.Diff<V> - Class in sbrt.kernel.math
Instances of this class are used to hold a variable and a pair of corresponding intervals.
IntervalComparison<V> - Class in sbrt.kernel.utilities.proc
This class is used to compare vectors of intervals.
IntervalComparison() - Constructor for class sbrt.kernel.utilities.proc.IntervalComparison
Constructs a new interval vector comparison process.
IntervalComparisonManager - Class in sbrt.shell.mng.utilities
This class is used to compare the intervals contained in separate files.
IntervalComparisonManager() - Constructor for class sbrt.shell.mng.utilities.IntervalComparisonManager
 
IntervalEquiv - Class in sbrt.kernel.math
This class is used to compare intervals for equivalence.
IntervalEquiv(double) - Constructor for class sbrt.kernel.math.IntervalEquiv
Creates a new interval equivalence tester with the provided tolerance.
IntervalFormat - Interface in sbrt.shell.text.math
This interface is used to represent formats for intervals.
IntervalFormatV1 - Class in sbrt.shell.text.math
This class is a concrete implementation of IntervalFormat.
IntervalFormatV1() - Constructor for class sbrt.shell.text.math.IntervalFormatV1
Constructs a new interval format.
IntervalVariationManager - Class in sbrt.shell.mng.fba
This abstract class provides utitlity functions for managing flux interval variation processes.
IntervalVariationManager() - Constructor for class sbrt.shell.mng.fba.IntervalVariationManager
 
InvalidFluxVectorException - Exception in sbrt.kernel.fba.comp
This class is used to indicate that a flux vector is invalid.
InvalidFluxVectorException(Map<String, Double>, double) - Constructor for exception sbrt.kernel.fba.comp.InvalidFluxVectorException
Constructs a new exception for the provided flux vector.
InvalidFluxVectorException(Map<String, Double>, double, String) - Constructor for exception sbrt.kernel.fba.comp.InvalidFluxVectorException
Constructs a new exception for the provided flux vector.
InvalidFluxVectorException(Map<String, Double>, double, Throwable) - Constructor for exception sbrt.kernel.fba.comp.InvalidFluxVectorException
Constructs a new exception for the provided flux vector.
InvalidFluxVectorException(Map<String, Double>, double, String, Throwable) - Constructor for exception sbrt.kernel.fba.comp.InvalidFluxVectorException
Constructs a new exception for the provided flux vector.
InvalidPointException - Exception in sbrt.kernel.math
This class is used to indicate that a point is invalid.
InvalidPointException(Map<?, ?>) - Constructor for exception sbrt.kernel.math.InvalidPointException
Constructs an exception to indicate the provided point is invalid.
InvalidPointException(Map<?, ?>, String) - Constructor for exception sbrt.kernel.math.InvalidPointException
Constructs an exception to indicate the provided point is invalid.
IrfFormatV1 - Class in sbrt.shell.text.fba
This class is used to format irreversible reaction fluxome files.
IrfFormatV1() - Constructor for class sbrt.shell.text.fba.IrfFormatV1
Constructs a new irreversible reaction fluxome format.
IRREV - Static variable in class sbrt.kernel.fba.MixedFluxomeV1
The constraint used by default for irreversible internal reactions and sink reactions: [0, Infinity).
IRREV_CONSTRAINT - Static variable in class sbrt.shell.mng.fba.RandomConstraintsManager
The keyword used to denote the constraint for irreversible reactions.
IrrevRxn - Class in sbrt.kernel.fba
This class is used to represent irreversible chemical reactions.
IrrevRxn(LinearComb<String>, LinearComb<String>) - Constructor for class sbrt.kernel.fba.IrrevRxn
Constructs a new irreversible reaction from the provided reactants and products.
IrrevRxnFluxome - Interface in sbrt.kernel.fba
This interface is used to represent fluxomes that contain only irreversible reactions.
IrrevRxnFluxomeV1 - Class in sbrt.kernel.fba
This class is a concrete implementation of IrrevRxnFluxome.
IrrevRxnFluxomeV1(Map<String, IrrevRxn>, Map<String, SourceRxn>, Map<String, SinkRxn>, Map<String, Or<And<String>>>) - Constructor for class sbrt.kernel.fba.IrrevRxnFluxomeV1
Constructs a new irreversible reaction fluxome from the provided internal and exchange reactions and catalysts.
IrrevRxnFluxomeV1(Map<String, IrrevRxn>, Map<String, SourceRxn>, Map<String, SinkRxn>) - Constructor for class sbrt.kernel.fba.IrrevRxnFluxomeV1
Constructs a new irreversible reaction fluxome from the provided internal and exchange reactions.
IrrevRxnFluxomeV1(Map<String, ? extends ChemRxn>, Map<String, Or<And<String>>>) - Constructor for class sbrt.kernel.fba.IrrevRxnFluxomeV1
Constructs a new irreversible reaction fluxome from the provided internal and exchange reactions and catalysts.
IrrevRxnFluxomeV1(Map<String, ? extends ChemRxn>) - Constructor for class sbrt.kernel.fba.IrrevRxnFluxomeV1
Constructs a new irreversible reaction fluxome from the provided internal and exchange reactions.
IrrevRxnFormatV1 - Class in sbrt.shell.text.chem
This class is used to format irreversible chemical reactions.
IrrevRxnFormatV1() - Constructor for class sbrt.shell.text.chem.IrrevRxnFormatV1
Constructs a new irreversible reaction format.
IrrevRxnFormatV1 - Class in sbrt.shell.text.fba
This class is used to format irreversible reactions for use in flux balance analysis.
IrrevRxnFormatV1() - Constructor for class sbrt.shell.text.fba.IrrevRxnFormatV1
Constructs a new irreversible reaction format.
IrrevRxnFormatV2 - Class in sbrt.shell.text.fba
This class is used to format irreversible reactions for use in flux balance analysis.
IrrevRxnFormatV2() - Constructor for class sbrt.shell.text.fba.IrrevRxnFormatV2
Constructs a new irreversible reaction format.
isCatalyst(String) - Method in interface sbrt.kernel.fba.CatalyzedFluxome
Indicates if the provided string is the name of a catalyst contained in this fluxome.
isCatalyst(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Indicates if the provided string is the name of an catalyst contained in this fluxome.
isCatalyst(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Indicates if the provided string is the name of an catalyst contained in this fluxome.
isClosed() - Method in class sbrt.kernel.io.AbstractResultsManager
Indicates if this results manager has already been closed.
isClosed() - Method in interface sbrt.kernel.io.ResultsManager
Indicates if this results manager has already been closed.
isClosed() - Method in class sbrt.shell.io.AbstractMapInputFile
Indicates if this file has already been closed.
isClosed() - Method in class sbrt.shell.io.AbstractMapOutputFile
Indicates if this file has already been closed.
isClosed() - Method in class sbrt.shell.io.fba.ColumnOrFbaOptOutputFile
Indicates if this file has already been closed.
isClosed() - Method in class sbrt.shell.io.fba.FluxCapInputFile
Indicates if this file has already been closed.
isClosed() - Method in class sbrt.shell.io.fba.FluxIntervalInputFile
Indicates if this file has already been closed.
isClosed() - Method in class sbrt.shell.io.fba.RowOrFbaOptOutputFile
Indicates if this file has already been closed.
isClosed() - Method in class sbrt.shell.io.fba.SerFbaOptOutputFile
Indicates if this file has already been closed.
isClosed() - Method in class sbrt.shell.io.MultiOutputFiles
Indicates if this results manager has already been closed.
isClosed() - Method in interface sbrt.shell.io.SbrtFile
Indicates if this file has already been closed.
isClosed() - Method in class sbrt.shell.io.SerializedFileIterator
Indicates if this iterator has been closed.
isClosed() - Method in class sbrt.shell.io.SerializedInputFile
Indicates if this file has already been closed.
isClosed() - Method in class sbrt.shell.io.SerializedOutputFile
Indicates if this file has already been closed.
isClosed() - Method in class sbrt.shell.io.TextFileLineIterator
Indicates if this iterator has been closed.
isClosed() - Method in class sbrt.shell.io.TextInputFile
Indicates if this file has already been closed.
isClosed() - Method in class sbrt.shell.io.TextOutputFile
Indicates if this file has already been closed.
isColumnIndex(Object) - Method in class sbrt.kernel.math.algebra.HashMatrix
Indicates if the provided object is a column index in this matrix.
isColumnIndex(Object) - Method in interface sbrt.kernel.math.algebra.Matrix
Indicates if the provided object is a column index in this matrix.
isColumnIndex(Object) - Method in class sbrt.kernel.math.algebra.MatrixWrap
Indicates if the provided object is a column index in this matrix.
isColumnIndex(Object) - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Indicates if the provided object is a column index in this matrix.
isColumnIndex(Object) - Method in class sbrt.kernel.math.algebra.TreeMatrix
Indicates if the provided object is a column index in this matrix.
isColumnVar(Object) - Method in class sbrt.ext.cplex.CplexSolver
Indicates if the provided object is a column variable in the matrix of this program solver.
isColumnVar(Object) - Method in class sbrt.ext.glpk.GlpkSolver
Indicates if the provided object is a column variable in the matrix of this program solver.
isColumnVar(Object) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Indicates if the provided object is a column variable in the matrix of this program solver.
isEdge(Object, Object) - Method in class sbrt.kernel.math.graph_theory.DirectedGraph
Indicates if an edge exists between the provided nodes.
isEmpty() - Method in class sbrt.kernel.math.algebra.AbstractMdMatrix
Indicates if this matrix is empty.
isEmpty() - Method in interface sbrt.kernel.math.algebra.Matrix
Indicates if this matrix is empty.
isEmpty() - Method in class sbrt.kernel.math.algebra.MatrixWrap
Indicates if this matrix is empty.
isEmpty() - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.isEmpty().
isEmpty() - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.isEmpty().
isEmpty() - Method in class sbrt.kernel.utilities.UnmodifiableMap
See Map.isEmpty().
isEmpty() - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.isEmpty().
isEof(Object) - Static method in class sbrt.shell.io.EndOfFile
Indicates if the provided object is an instance of this class.
isEof(Object) - Static method in class sbrt.shell.io.SerializedOutputFile
Indicates if the provided object is a valid end-of-file marker.
isExchangeRxnName(String) - Method in interface sbrt.kernel.fba.Fluxome
Indicates if the provided string is the name of an exchange reaction contained in this fluxome.
isExchangeRxnName(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Indicates if the provided string is the name of an exchange reaction contained in this fluxome.
isExchangeRxnName(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Indicates if the provided string is the name of an exchange reaction contained in this fluxome.
isFluxVector(Map<String, Double>, double) - Method in interface sbrt.kernel.fba.Fluxome
Indicates if the provided flux vector lies within the feasible space of this fluxome, given the provided tolerance value.
isFluxVector(Map<String, Double>, double) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Indicates if the provided flux vector lies within the feasible space of this fluxome, given the provided tolerance value.
isFluxVector(Map<String, Double>, double) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Indicates if the provided flux vector lies within the feasible space of this fluxome, given the provided tolerance value.
isInternalRxnName(String) - Method in interface sbrt.kernel.fba.Fluxome
Indicates if the provided string is the name of an internal reaction contained in this fluxome.
isInternalRxnName(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Indicates if the provided string is the name of an internal reaction contained in this fluxome.
isInternalRxnName(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Indicates if the provided string is the name of an internal reaction contained in this fluxome.
isKey(Object) - Static method in class sbrt.ext.R.R
Indicates if the provided object is the key to unlock the R engine.
isLocked() - Static method in class sbrt.ext.R.R
Indicates if the R engine is currently locked.
isNode(Object) - Method in class sbrt.kernel.math.graph_theory.DirectedGraph
Indicates if the provided object is a node in this graph.
isObjValueHeader(String) - Method in interface sbrt.shell.text.fba.FbaOptFileLineFormat
Indicates if the provided string is the header used to indicate the value of the objective function.
isObjValueHeader(String) - Method in class sbrt.shell.text.fba.FbaOptFileLineFormatV1
Indicates if the provided string is the header used to indicate the value of the objective function.
isObjValueHeader(String) - Method in interface sbrt.shell.text.fba.FbaOptHeaderFormatter
Indicates if the provided string is the header used to indicate the value of the objective function.
isObjValueHeader(String) - Method in class sbrt.shell.text.fba.FbaOptHeaderFormatterV1
Indicates if the provided string is the header used to indicate the value of the objective function.
isObjValueHeader(String) - Method in interface sbrt.shell.text.fba.FbaOptHeaderParser
Indicates if the provided string is the header used to indicate the value of the objective function.
isObjValueHeader(String) - Method in class sbrt.shell.text.fba.FbaOptHeaderParserV1
Indicates if the provided string is the header used to indicate the value of the objective function.
isReqCatalyst(String, String) - Method in interface sbrt.kernel.fba.CatalyzedFluxome
Indicates if the provided catalyst is required for the reaction with the provided name.
isReqCatalyst(String, String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Indicates if the specified catalyst is required for the reaction with the specified name.
isReqCatalyst(String, String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Indicates if the specified catalyst is required for the reaction with the specified name.
isReversible() - Method in interface sbrt.kernel.fba.ChemRxn
Indicates if this chemical reaction is considered reversible.
isReversible() - Method in class sbrt.kernel.fba.IrrevRxn
Returns false.
isReversible() - Method in class sbrt.kernel.fba.RevExchRxn
Returns true.
isReversible() - Method in class sbrt.kernel.fba.RevRxn
Returns true.
isReversible() - Method in class sbrt.kernel.fba.SinkRxn
Returns false.
isReversible() - Method in class sbrt.kernel.fba.SourceRxn
Returns false.
isReversible(Node) - Method in class sbrt.shell.text.fba.BiggRxnNodeParser
Indicates if the reaction in the provided reaction node is reversible.
isReversible(Node) - Method in class sbrt.shell.text.fba.PalssonRxnNodeParser
Indicates if the reaction in the provided reaction node is reversible.
isRowIndex(Object) - Method in class sbrt.kernel.math.algebra.HashMatrix
Indicates if the provided object is a row index in this matrix.
isRowIndex(Object) - Method in interface sbrt.kernel.math.algebra.Matrix
Indicates if the provided object is a row index in this matrix.
isRowIndex(Object) - Method in class sbrt.kernel.math.algebra.MatrixWrap
Indicates if the provided object is a row index in this matrix.
isRowIndex(Object) - Method in class sbrt.kernel.math.algebra.RowOrTreeMatrix
Indicates if the provided object is a row index in this matrix.
isRowIndex(Object) - Method in class sbrt.kernel.math.algebra.TreeMatrix
Indicates if the provided object is a row index in this matrix.
isRowVar(Object) - Method in class sbrt.ext.cplex.CplexSolver
Indicates if the provided object is a row variable in the matrix of this program solver.
isRowVar(Object) - Method in class sbrt.ext.glpk.GlpkSolver
Indicates if the provided object is a row variable in the matrix of this program solver.
isRowVar(Object) - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Indicates if the provided object is a row variable in the matrix of this program solver.
isRxnName(String) - Method in interface sbrt.kernel.fba.Fluxome
Indicates if the provided string is the name of a reaction contained in this fluxome.
isRxnName(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Indicates if the provided string is the name of a reaction contained in this fluxome.
isRxnName(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Indicates if the provided string is the name of a reaction contained in this fluxome.
isSinkRxnName(String) - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Indicates if the provided string is the name of a sink reaction contained in this fluxome.
isSinkRxnName(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Indicates if the provided string is the name of a sink reaction contained in this fluxome.
isSolutionVector(Map<?, Double>, double) - Method in class sbrt.kernel.math.algebra.HashLinearSystemSolution
Indicates if the provided solution vector is consistent with this solution.
isSolutionVector(Map<?, Double>, double) - Method in interface sbrt.kernel.math.algebra.LinearSystemSolution
Indicates if the provided solution vector is consistent with this solution.
isSourceRxnName(String) - Method in interface sbrt.kernel.fba.IrrevRxnFluxome
Indicates if the provided string is the name of a source reaction contained in this fluxome.
isSourceRxnName(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Indicates if the provided string is the name of a source reaction contained in this fluxome.
isSpecies(String) - Method in interface sbrt.kernel.fba.Fluxome
Indicates if the provided string is the name of a chemical species contained in this fluxome.
isSpecies(String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Indicates if the provided string is the name of a chemical species contained in this fluxome.
isSpecies(String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Indicates if the provided string is the name of a chemical species contained in this fluxome.
isValid(Interval, String, double) - Method in interface sbrt.kernel.fba.Fluxome
Indicates if the provided interval is a valid flux constraint for the reaction with the provided name.
isValid(Interval, String, double) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Indicates if the provided interval is a valid flux constraint for the reaction having the provided name.
isValid(Interval, String, double) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Indicates if the provided interval is a valid flux constraint for the reaction having the provided name.
isValidFormat(FileFormat) - Static method in class sbrt.shell.io.SerializedFileIterator
Indicates if the provided file format is valid for this type of file iterator.
isValidFormat(FileFormat) - Static method in class sbrt.shell.io.SerializedInputFile
Indicates if the provided file format is valid for a text input file.
isValidFormat(FileFormat) - Static method in class sbrt.shell.io.SerializedOutputFile
Indicates if the provided file format is valid for a serialized output file.
isValidFormat(FileFormat) - Static method in class sbrt.shell.io.TextFileLineIterator
Indicates if the provided file format is valid for this type of file line iterator.
isValidFormat(FileFormat) - Static method in class sbrt.shell.io.TextInputFile
Indicates if the provided file format is valid for a text input file.
isValidFormat(FileFormat) - Static method in class sbrt.shell.io.TextOutputFile
Indicates if the provided file format is valid for a text output file.
isVariable(Object) - Method in class sbrt.kernel.math.algebra.HashLinearSystemSolution
Indicates if the provided object is a variable in this solution.
isVariable(Object) - Method in interface sbrt.kernel.math.algebra.LinearSystemSolution
Indicates if the provided object is a variable in this solution.
isVariable(Object) - Method in interface sbrt.kernel.math.geom.ConvexPolytope
Indicates if the provided object is a variable in the bounding hyperplanes of this convex polytope.
isVariable(Object) - Method in class sbrt.kernel.math.geom.HashConvexPolytope
Indicates if the provided object is a variable in the bounding hyperplanes of this convex polytope.
isWithin(Map<? extends V, Double>, double) - Method in interface sbrt.kernel.math.geom.ConvexPolytope
Indicates if the provided point lies within this convex polytope.
isWithin(Map<? extends V, Double>, double) - Method in class sbrt.kernel.math.geom.HashConvexPolytope
Indicates if the provided point lies within this convex polytope.
isWithin(double) - Method in class sbrt.kernel.math.Interval
Indicates if the provided value lies within this interval.
isWithin(double, double) - Method in class sbrt.kernel.math.Interval
Indicates if the provided value lies within this interval, given the provided numerical tolerance.
isZero(double) - Static method in class sbrt.kernel.utilities.Util
Indicates if the provided value equals 0.
ITERATIONS - Static variable in class sbrt.shell.mng.AbstractProcessManager
The keyword used to denote the number of iterations.
iterator() - Method in class sbrt.kernel.io.ListResultsManager
Returns an iterator over the list of results.
iterator() - Method in class sbrt.kernel.math.AbstractLinearComb
Returns an iterator over the terms of this linear combination.
iterator() - Method in class sbrt.kernel.math.AbstractLinearComb.Term
Returns an iterator over the variables in this term.
iterator() - Method in class sbrt.kernel.math.graph_theory.Path
Returns an iterator over the nodes in this path in proper sequence.
iterator() - Method in class sbrt.kernel.math.HashLinearComb
Returns an iterator over the terms of this linear combination.
iterator() - Method in interface sbrt.kernel.math.LinearComb
Returns an iterator over the terms of this linear combination.
iterator() - Method in interface sbrt.kernel.math.Polynomial.Term
Returns an iterator over the variables in this term.
iterator() - Method in class sbrt.kernel.utilities.LogicalRelation
Returns an iterator over the conditions of this logical relationship.
iterator() - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.iterator().
iterator() - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.iterator().
iterator() - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.iterator().
iterator() - Method in class sbrt.shell.io.ComiFile
Returns an iterator over this file.
iterator(int) - Method in class sbrt.shell.io.ComiFile
Returns an iterator over this file beginning at the specified index.
iterator() - Method in class sbrt.shell.io.fba.FluxCapInputFile
Returns an iterator over this file.
iterator() - Method in class sbrt.shell.io.fba.FluxIntervalInputFile
Returns an iterator over the flux intervals contained in this file.
iterator() - Method in class sbrt.shell.io.fba.RxnNamExprSetInputFile
Returns an iterator over the set of reaction name expressions contained in this file.
iterator() - Method in class sbrt.shell.io.RomiFile
Returns an iterator over this file.
iterator() - Method in class sbrt.shell.io.SerializedInputFile
Returns an object iterator over this file.
iterator() - Method in class sbrt.shell.io.SerializedMapInputFile
Returns an iterator over this file.
iterator() - Method in class sbrt.shell.io.TextInputFile
Returns a line iterator over this text file.
iterator(int) - Method in class sbrt.shell.io.TextInputFile
Returns a line iterator over this text file beginning at the specified line.

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