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

E

EDGE_FILE - Static variable in class sbrt.shell.mng.graph_theory.CycleIdManager
The keyword used to denote the input file containing a set of edges.
EDGE_FILE - Static variable in class sbrt.shell.mng.graph_theory.PathIdManager
The keyword used to denote the input file containing a set of edges.
edges() - Method in class sbrt.kernel.math.graph_theory.DirectedGraph
Returns the number of edges in this graph.
ELAPSED_TIME - Static variable in class sbrt.shell.mng.AbstractProcessManager
The prefix used to denote the amount of time that has elapsed since an operation was started.
ELEM_MODE_FILE_NAME - Static variable in class sbrt.shell.mng.fba.MetatoolOutputReaderManager
The keyword used to denote the name of a file to which elementary modes are written.
elements() - Method in class sbrt.kernel.utilities.LogicalRelation
Returns the number of conditions of this logical relationship.
EndOfFile - Class in sbrt.shell.io
This class is used to represent end-of-file (EOF).
entrySet() - Method in class sbrt.kernel.utilities.UnmodifiableMap
See Map.entrySet().
ENZIRREV - Static variable in class sbrt.shell.proc.fba.MetatoolInputReader
The Metatool keyword -ENZIRREV.
ENZREV - Static variable in class sbrt.shell.proc.fba.MetatoolInputReader
The Metatool keyword -ENZREV.
equal(double, double, double) - Static method in class sbrt.kernel.utilities.Util
Indicates if the provided values are equal to each other, given the provided tolerance.
equals(Object) - Method in class sbrt.kernel.fba.AbstractExchangeRxn
Returns obj == this.
equals(Object) - Method in class sbrt.kernel.fba.AbstractRxn
Returns obj == this.
equals(Object) - Method in interface sbrt.kernel.fba.ChemRxn
Indicates if the provided object is "equal to" this chemical reaction.
equals(Object) - Method in class sbrt.kernel.math.AbstractLinearComb
Indicates if the provided object is equal to this linear combination.
equals(Object) - Method in class sbrt.kernel.math.AbstractLinearComb.Term
Indicates if the provided object is equal to this term.
equals(Object) - Method in class sbrt.kernel.math.algebra.AbstractMdMatrix
Indicates if the provided object is equal to this matrix.
equals(Object) - Method in class sbrt.kernel.math.algebra.AbstractSmdMatrix
Indicates if the provided object is equal to this matrix.
equals(Object) - Method in class sbrt.kernel.math.algebra.IndexPair
Indicates if this index pair is equal to the provided object.
equals(Object) - Method in interface sbrt.kernel.math.algebra.Matrix
Indicates if the provided object is equal to this matrix.
equals(Object) - Method in class sbrt.kernel.math.algebra.MatrixElement
Indicates if this matrix element is equal to the provided object.
equals(Object) - Method in class sbrt.kernel.math.algebra.MatrixWrap
Indicates if the provided object is equal to this matrix.
equals(Object) - Method in class sbrt.kernel.math.geom.ParallelHyperplanes
Indicates if the provided object is equal to this pair of bounding parallelt hyperplanes.
equals(Object) - Method in class sbrt.kernel.math.graph_theory.DirectedGraph.Edge
Indicates if the provided object is equal to this directed edge.
equals(Object) - Method in class sbrt.kernel.math.graph_theory.Path
Compares the specified object with this path for equality.
equals(Object) - Method in class sbrt.kernel.math.Interval
Indicates if the provided object is equal to this interval.
equals(Object) - Method in interface sbrt.kernel.math.LinearComb
Indicates if the provided object is equal to this linear combination.
equals(Object) - Method in interface sbrt.kernel.math.MathExpr
Indicates if the provided object is equal to this mathematical expression.
equals(Object) - Method in interface sbrt.kernel.math.Polynomial
Indicates if the provided object is equal to this polynomial.
equals(Object) - Method in interface sbrt.kernel.math.Polynomial.Term
Indicates if the provided object is equal to this term.
equals(Object) - Method in class sbrt.kernel.math.stat.comp.MannWhitneyResults
Indicates if the provided object is equal to this results object.
equals(Object) - Method in class sbrt.kernel.math.stat.comp.TauResult
Indicates if the provided object is equal to this correlation results object.
equals(Object) - Method in class sbrt.kernel.utilities.And
Indicates if this "and" is equal to the provided object.
equals(Object) - Method in class sbrt.kernel.utilities.LogicalRelation
Inidicates if this logical relationship is "equal to" the provided object.
equals(Object) - Method in class sbrt.kernel.utilities.Or
Indicates if this "or" is equal to the provided object.
equals(Object) - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.equals(Object).
equals(Object) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.equals(Object).
equals(Object) - Method in class sbrt.kernel.utilities.UnmodifiableMap
See Map.equals(Object).
equals(Object) - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.equals(Object).
equals(Object) - Method in class sbrt.shell.io.EndOfFile
Indicates if the provided object is equal to this end-of-file.
EQUALS - Static variable in class sbrt.shell.text.SpecialChars
=
EqualsMapEntryFormatV1<K,V> - Class in sbrt.shell.text
This class is a concrete implementation of MapEntryFormat.
EqualsMapEntryFormatV1(SimpleFormat<K>, SimpleFormat<V>) - Constructor for class sbrt.shell.text.EqualsMapEntryFormatV1
Constructs a new map format using the provided key and value formats.
EqualsMapFormatV1<K,V> - Class in sbrt.shell.text
This class is a concrete implementation of MapFormat.
EqualsMapFormatV1(Formatter<K>, Parser<K>, Formatter<V>, Parser<V>) - Constructor for class sbrt.shell.text.EqualsMapFormatV1
Constructs a new map format using the provided key and value formats.
EqualsMapFormatV1(SimpleFormat<K>, SimpleFormat<V>) - Constructor for class sbrt.shell.text.EqualsMapFormatV1
Constructs a new map format using the provided key and value formats.
EQUATION_FILE_NAME - Static variable in class sbrt.shell.mng.fba.NetworkInfoManager
The keyword used to denote the name of the file to which the system of linear equations formed by a fluxome will be written.
EQUATIONS_FILE - Static variable in class sbrt.shell.mng.algebra.LinearSolverManager
The keyword used to denote the name of the file containing the system of linear equations.
EQUIV_RXN_FILE_NAME - Static variable in class sbrt.shell.mng.fba.NetworkInfoManager
The keyword used to denote the name of the file to which stoichiometrically equivalent reactions will be written.
equivChemRxns(ChemRxn, ChemRxn) - Static method in class sbrt.kernel.fba.RxnComparer
Indicates if the provided chemical reactions are stoichiometrically equivalent.
equivIrrevRxns(IrrevRxn, IrrevRxn) - Static method in class sbrt.kernel.fba.RxnComparer
Indicates if the provided irreversible reactions are stoichiometrically equivalent.
equivRevExchRxns(RevExchRxn, RevExchRxn) - Static method in class sbrt.kernel.fba.RxnComparer
Indicates if the provided reversible exchange reactions are stoichiometrically equivalent.
equivRevRxns(RevRxn, RevRxn) - Static method in class sbrt.kernel.fba.RxnComparer
Indicates if the provided reversible reactions are stoichiometrically equivalent.
equivSinkRxns(SinkRxn, SinkRxn) - Static method in class sbrt.kernel.fba.RxnComparer
Indicates if the provided sink reactions are stoichiometrically equivalent.
equivSourceRxns(SourceRxn, SourceRxn) - Static method in class sbrt.kernel.fba.RxnComparer
Indicates if the provided source reactions are stoichiometrically equivalent.
EquivTester<T> - Interface in sbrt.kernel.math
This interface is used to represent equivalence testers.
ERROR_LOG - Static variable in class sbrt.ProcessRunner
The name of the file in which errors will be logged.
EuclideanDist - Class in sbrt.kernel.math.geom.comp
This class is used to compute Euclidean distances.
EuclideanDist() - Constructor for class sbrt.kernel.math.geom.comp.EuclideanDist
 
eval(String, Object) - Static method in class sbrt.ext.R.R
Evaluates the provided R command.
ExceededLimitException - Exception in sbrt.kernel.math
This class is used to indicate that a limit has been exceeded.
ExceededLimitException() - Constructor for exception sbrt.kernel.math.ExceededLimitException
 
ExchangeRxn - Interface in sbrt.kernel.fba
This interface is used to represent exchange reactions.
exchangeRxns() - Method in interface sbrt.kernel.fba.Fluxome
Returns the total number of exchange reactions contained in this fluxome.
exchangeRxns() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the total number of exchange reactions contained in this fluxome.
exchangeRxns() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the total number of exchange reactions contained in this fluxome.
EXCLAMATION - Static variable in class sbrt.shell.text.SpecialChars
!
execute(PrintWriter) - Method in class plug_in_example.shell.GreetingManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute() - Method in class sbrt.shell.mng.AbstractProcessManager
Executes the process this process manager controls.
execute(PrintWriter) - Method in class sbrt.shell.mng.algebra.LinearCombConverterManager
Executes the process this process manager controls and writes informative messages to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.algebra.LinearSolverManager
Executes the process this process manager controls and writes the results to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.algebra.MatrixConverterManager
Executes the process this process manager controls and writes informative messages to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.algebra.MultipleVectorsConverterManager
Executes the process this process manager controls and writes informative messages to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.algebra.SingleVectorConverterManager
Executes the process this process manager controls and writes informative messages to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.comb.SingleElementUnionManager
Executes the process this process manager controls and writes the results to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.comb.StrictSingleElementUnionManager
Executes the process this process manager controls and writes the results to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.BiggSbmlReaderManager
Executes the process this process manager controls and writes informative messages to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.CatalystDeletionManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.CdHarFluxVectorManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.CvCatalystDeletionManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.CvFbaOptManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.CvMsFluxIntervalManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.CvObjectiveFunctionManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.CvRevRxnFluxIntervalManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.CvRxnDeletionManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.CvSimpleFluxIntervalManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.ExtremeCurrentManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.FbaOptManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.FbaSolverManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.FluxActivityManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.FluxCapManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.FluxPlasticityManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.InitialPointManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.MetatoolInputReaderManager
Executes the process this process manager controls and writes informative messages to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.MetatoolInputWriterManager
Executes the process this process manager controls and writes informative messages to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.MetatoolOutputReaderManager
Executes the process this process manager controls and writes informative messages to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.MsFluxIntervalManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.MsFluxomeReducerManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.NetworkInfoManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.ObjectiveFunctionManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.PalssonSbmlReaderManager
Executes the process this process manager controls and writes informative messages to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.RandomConstraintsManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.RandomObjectiveManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.RedundRxnRemoverManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.ReverseRxnFluxIntervalManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.RevRxnBreakerManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.RxnDeletionManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.SimpleRxnFileTransManager
Executes the process this process manager controls and writes informative messages to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.SlpCycleIdManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.fba.WwFluxomeReducerManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.geom.CdHarManager
Executes the process this process manager controls and writes the results to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.graph_theory.CycleIdManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.graph_theory.GraphInfoManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.graph_theory.PathIdManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.graph_theory.UniqueCycleIdManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute() - Method in interface sbrt.shell.mng.ProcessManager
Executes the process this process manager controls.
execute(PrintWriter) - Method in interface sbrt.shell.mng.ProcessManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.stat.CorrelationManager
Executes the process this process manager controls and writes the results to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.stat.KendallTauManager
Executes the process this process manager controls and writes the results to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.stat.MannWhitneyUManager
Executes the process this process manager controls and writes the results to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.utilities.IntervalComparisonManager
Executes the process this process manager controls and writes informative messages to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.utilities.VariableParticipationManager
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer.
execute(PrintWriter) - Method in class sbrt.shell.mng.utilities.VectorComparisonManager
Executes the process this process manager controls and writes informative messages to the provided print writer.
EXPRESSION_FILE - Static variable in class sbrt.shell.mng.utilities.VariableParticipationManager
The keyword used to denote the input file containing mathematical expressions.
ExternalSoftwareException - Exception in sbrt.ext
This class is used to wrap exceptions thrown by external software packages.
ExternalSoftwareException(Throwable) - Constructor for exception sbrt.ext.ExternalSoftwareException
Constructs an external software exception.
ExternalSoftwareException(String, Throwable) - Constructor for exception sbrt.ext.ExternalSoftwareException
Constructs an external software exception.
ExtremeCurrentComputer - Interface in sbrt.kernel.fba.comp
This interface is used to represent extreme current computers.
ExtremeCurrentManager - Class in sbrt.shell.mng.fba
This class is used to manage FBA extreme current processes.
ExtremeCurrentManager() - Constructor for class sbrt.shell.mng.fba.ExtremeCurrentManager
 
ExtremeCurrentManager.Rm - Class in sbrt.shell.mng.fba
 
ExtremeCurrentManager.Rm(ComoFile<String, Double>) - Constructor for class sbrt.shell.mng.fba.ExtremeCurrentManager.Rm
Constructs a new results manager for writing extreme current matrices.
ExtremeCurrentProcess<F extends IrrevRxnFluxome> - Class in sbrt.kernel.fba.proc
This class is used to identify the extreme currents in stoichiometric networks.
ExtremeCurrentProcess(F, ExtremeCurrentComputer) - Constructor for class sbrt.kernel.fba.proc.ExtremeCurrentProcess
Constructs a new extreme current process.

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