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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.
Overview
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