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D
DASH
- Static variable in class sbrt.shell.text.
SpecialChars
-
DATA_HEADERS
- Static variable in class sbrt.shell.mng.
AbstractProcessManager
The keyword used to denote the data headers of, say, an output file.
debugPrintln(Object)
- Static method in class sbrt.kernel.utilities.
Util
Prints the provided object to System.err, preceded by a carriage return character.
DEFAULT_COEFF_CUTOFF
- Static variable in class sbrt.kernel.fba.comp.
CdHarFluxComp
The default zero cutoff for coefficients in linear combinations.
DEFAULT_CONST_TOL
- Static variable in class sbrt.kernel.fba.comp.
FbaOptimizer
The default constraint tolerance.
DEFAULT_CONSTRAINT_TOLERANCE
- Static variable in class sbrt.shell.mng.fba.
FbaManager
The default constraint tolerance.
DEFAULT_CONSTRAINT_TOLERANCE
- Static variable in class sbrt.shell.mng.geom.
CdHarManager
The default constraint tolerance.
DEFAULT_MIN_CHORD
- Static variable in class sbrt.kernel.fba.comp.
CdHarFluxComp
The default minimum chord length.
DEFAULT_MIN_CHORD_LENGTH
- Static variable in class sbrt.shell.mng.geom.
CdHarManager
The default constraint tolerance.
DEFAULT_P
- Static variable in class sbrt.shell.mng.fba.
InitialPointManager
The default P intercept value.
DEFAULT_SAFETY_LEVEL
- Static variable in class sbrt.kernel.fba.comp.
FbaOptimizer
The default saftey level.
DEFAULT_SAFETY_LEVEL
- Static variable in class sbrt.shell.mng.fba.
FbaOptManager
The default safety level used by
FbaOptManager.getSafetyLevel(ManagerInput, PrintWriter)
.
DEFAULT_TOLERANCE
- Static variable in class sbrt.kernel.fba.comp.
CdHarFluxComp
The default constraint tolerance.
DEFAULT_ZERO_CUTOFF
- Variable in class sbrt.kernel.fba.comp.
InitialPointComputer
The default zero cutoff.
delete(Set<String>)
- Method in class sbrt.kernel.fba.comp.
RxnDeletionComputer
Computes and returns the results of deleting the reactions whose names appear in the provided set.
DEV_NULL
- Static variable in class sbrt.shell.mng.
AbstractProcessManager
A print writer that discards all data it receives.
DevNull
- Class in
sbrt.shell.io
This class is used to mimic /dev/null from Unix-like operating systems.
DimensionException
- Exception in
sbrt.kernel.math.geom
This class is used to indicate invalid dimensions.
DimensionException(int)
- Constructor for exception sbrt.kernel.math.geom.
DimensionException
Constructs a new dimension exception.
dimensions()
- Method in interface sbrt.kernel.math.geom.
ConvexPolytope
Returns the dimensions of the space in which this polytope lies.
dimensions()
- Method in class sbrt.kernel.math.geom.
HashConvexPolytope
Returns the dimensions of the space in which this polytope lies.
DirectedGraph
<
N
> - Class in
sbrt.kernel.math.graph_theory
This class is used to represent directed graphs.
DirectedGraph(Set<DirectedGraph.Edge<N>>)
- Constructor for class sbrt.kernel.math.graph_theory.
DirectedGraph
Constructs a new directed graph from the provided collection of edges.
DirectedGraph.Edge
<
N
> - Class in
sbrt.kernel.math.graph_theory
This class is used to represent the unidirectional edges of a directed graph.
DirectedGraph.Edge(T, S)
- Constructor for class sbrt.kernel.math.graph_theory.
DirectedGraph.Edge
Constructs a new directed edge from the provided source and sink nodes.
DirEdgeFormat
<
N
> - Interface in
sbrt.shell.text.math
This interface is used to represent formats for the edges of directed graphs.
DirEdgeFormatV1
<
N
> - Class in
sbrt.shell.text.math
This class is a concrete implementation of
DirEdgeFormat
.
DirEdgeFormatV1(SimpleFormat<N>)
- Constructor for class sbrt.shell.text.math.
DirEdgeFormatV1
Constructs a new directed edge format.
DiscreteProgressMonitor
- Class in
sbrt.kernel.utilities
This class is used to monitor the progress of a process that occurs in discrete events.
DiscreteProgressMonitor()
- Constructor for class sbrt.kernel.utilities.
DiscreteProgressMonitor
Constructs a new discrete progress monitor.
DOLLAR
- Static variable in class sbrt.shell.text.
SpecialChars
$
DOT
- Static variable in class sbrt.shell.text.
SpecialChars
.
DoubleEquiv
- Class in
sbrt.kernel.math
This class is used to compare double precision numbers for equivalence.
DoubleEquiv(double)
- Constructor for class sbrt.kernel.math.
DoubleEquiv
Creates a new double precision number equivalence tester with the provided tolerance.
DoubleFormat
- Interface in
sbrt.shell.text
This interface is used to represent a format for double precision numbers.
DoubleFormatV1
- Class in
sbrt.shell.text
This class is a concrete implementation of
DoubleFormat
.
DoubleFormatV1()
- Constructor for class sbrt.shell.text.
DoubleFormatV1
DoubleFormatV2
- Class in
sbrt.shell.text
This class is a concrete implementation of
DoubleFormat
.
DoubleFormatV2()
- Constructor for class sbrt.shell.text.
DoubleFormatV2
Constructs a new double format for finite numbers.
DoubleMatrix
<
R
,
C
> - Interface in
sbrt.kernel.math.algebra
This interface is used to represent matrices whose elements are strictly double precision numbers.
DoubleMatrixBuilder
<
R
,
C
> - Interface in
sbrt.kernel.math.algebra
This interface is used to represent mutable matrices whose elements are strictly double precision numbers.
DoubleMatrixWrap
<
R
,
C
> - Class in
sbrt.kernel.math.algebra
This class is used to wrap mutable matrices as an immutable
DoubleMatrix
.
DoubleMatrixWrap(DoubleMatrix<R, C>)
- Constructor for class sbrt.kernel.math.algebra.
DoubleMatrixWrap
Constructs a new wrapper around the provided matrix.
DummyConsole
- Class in
sbrt.ext.R
This class is used to make dummy consoles for the JRI.
DummyConsole()
- Constructor for class sbrt.ext.R.
DummyConsole
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