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nameClassMap
- Static variable in class sbrt.shell.
ProgramSolverFactory
The correspondence between the strings used to denote a particular program solver and the name of the actual class it represents.
neighbors(Object)
- Method in class sbrt.kernel.math.graph_theory.
DirectedGraph
Returns the number of nodes neighboring the provided node.
NetworkInfoManager
- Class in
sbrt.shell.mng.fba
This class is used to manage fluxome information processes.
NetworkInfoManager()
- Constructor for class sbrt.shell.mng.fba.
NetworkInfoManager
NetworkInfoProcess
<
F
extends
CatalyzedFluxome
> - Class in
sbrt.kernel.fba.proc
This class is used to gather basic information about a fluxome.
NetworkInfoProcess(F)
- Constructor for class sbrt.kernel.fba.proc.
NetworkInfoProcess
Constructs a new network information gatherer process.
NetworkInfoProcess.Results
<
F
extends
CatalyzedFluxome
> - Class in
sbrt.kernel.fba.proc
This class is used to represent the information gathered about a fluxome.
NEVER_ACTIVE_FILE_NAME
- Static variable in class sbrt.shell.mng.fba.
FluxPlasticityManager
The keyword used to denote the name of the output file for the names of never-active reactions.
neverActive()
- Method in class sbrt.kernel.fba.proc.
FluxPlasticityProcess.Results
Returns the number of fluxes that are never active.
next()
- Method in class sbrt.kernel.math.geom.comp.
CdHarComp
Computes and returns the next random interior point of the convex polytope.
next(int)
- Method in class sbrt.kernel.math.geom.comp.
CdHarComp
Computes the specified number of random interior points, and returns the last one computed.
next()
- Method in class sbrt.kernel.utilities.
UnmodifiableIterator
See Iterator.next().
next()
- Method in class sbrt.shell.io.
ComiFileSource
Returns the next column-oriented map input file with the next name returned by the file name source.
next()
- Method in class sbrt.shell.io.
ComoFileSource
Returns the next column-oriented map output file with the next name returned by the file name source.
next()
- Method in class sbrt.shell.io.fba.
CofoofSource
Returns the next column-oriented map output file with the next name returned by the file name source.
next()
- Method in class sbrt.shell.io.fba.
RofoofSource
Returns the next row-oriented map output file with the next name returned by the file name source.
next()
- Method in class sbrt.shell.io.fba.
SfoofSource
Returns the next serialized map output file with the next name returned by the file name source.
next()
- Method in class sbrt.shell.io.
RomiFileSource
Returns the next row-oriented map input file with the next name returned by the file name source.
next()
- Method in class sbrt.shell.io.
RomoFileSource
Returns the next row-oriented map output file with the next name returned by the file name source.
next()
- Method in class sbrt.shell.io.
SerializedFileIterator
Returns the next object in the file.
next()
- Method in class sbrt.shell.io.
SmoFileSource
Returns the next column-oriented map output file with the next name returned by the file name source.
next()
- Method in class sbrt.shell.io.
TextFileLineIterator
Returns the next element in the file.
nextObject()
- Method in class sbrt.shell.io.
SerializedFileIterator
Returns the next object in the file.
NODE_FILE_NAME
- Static variable in class sbrt.shell.mng.graph_theory.
GraphInfoManager
The keyword used to denote the name of the file to which all nodes will be written.
nodes()
- Method in class sbrt.kernel.math.graph_theory.
DirectedGraph
Returns the number of nodes in this graph.
nodes()
- Method in class sbrt.kernel.math.graph_theory.
Path
Returns the number of nodes in this path.
NonEmptyStringFormat
- Class in
sbrt.shell.text
This class is used to define a format for
String
objects.
NonEmptyStringFormat()
- Constructor for class sbrt.shell.text.
NonEmptyStringFormat
NormalDist
- Class in
sbrt.kernel.math.stat
This class is used to represent normal distributions.
NormalDist(double, double)
- Constructor for class sbrt.kernel.math.stat.
NormalDist
Constructs a new normal distribution with the provided average and standard deviation.
NOT_PROVIDED
- Static variable in class sbrt.shell.proc.fba.
PalssonSbmlReader
The string used to denote that a particular value was not provided in an SBML input file.
nullCheck(Object)
- Static method in class sbrt.kernel.utilities.
Util
Ensures the provided object is not null.
NUM_ACTIVE_FLUXES
- Static variable in class sbrt.shell.mng.fba.
RandomConstraintsManager
The keyword used to denote the number of active fluxes.
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