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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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