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Hierarchy For All Packages
Package Hierarchies:
plug_in_example.kernel
,
plug_in_example.shell
,
sbrt
,
sbrt.ext
,
sbrt.ext.cplex
,
sbrt.ext.glpk
,
sbrt.ext.mma
,
sbrt.ext.mma.algebra
,
sbrt.ext.R
,
sbrt.ext.R.stat
,
sbrt.kernel
,
sbrt.kernel.fba
,
sbrt.kernel.fba.analysis
,
sbrt.kernel.fba.comp
,
sbrt.kernel.fba.proc
,
sbrt.kernel.io
,
sbrt.kernel.math
,
sbrt.kernel.math.algebra
,
sbrt.kernel.math.algebra.proc
,
sbrt.kernel.math.comb.comp
,
sbrt.kernel.math.comb.proc
,
sbrt.kernel.math.geom
,
sbrt.kernel.math.geom.comp
,
sbrt.kernel.math.geom.proc
,
sbrt.kernel.math.graph_theory
,
sbrt.kernel.math.graph_theory.comp
,
sbrt.kernel.math.graph_theory.proc
,
sbrt.kernel.math.optimization
,
sbrt.kernel.math.stat
,
sbrt.kernel.math.stat.comp
,
sbrt.kernel.math.stat.proc
,
sbrt.kernel.utilities
,
sbrt.kernel.utilities.proc
,
sbrt.shell
,
sbrt.shell.gui
,
sbrt.shell.io
,
sbrt.shell.io.fba
,
sbrt.shell.mng
,
sbrt.shell.mng.algebra
,
sbrt.shell.mng.comb
,
sbrt.shell.mng.fba
,
sbrt.shell.mng.geom
,
sbrt.shell.mng.graph_theory
,
sbrt.shell.mng.stat
,
sbrt.shell.mng.utilities
,
sbrt.shell.proc.fba
,
sbrt.shell.text
,
sbrt.shell.text.chem
,
sbrt.shell.text.fba
,
sbrt.shell.text.math
Class Hierarchy
java.lang.Object
sbrt.kernel.fba.comp.
AbstractCvComputer
<F> (implements sbrt.kernel.fba.comp.
FluxCvComputer
<F>)
sbrt.kernel.fba.comp.
AbstractFluxIntervalComputer
<F> (implements sbrt.kernel.fba.comp.
FluxIntervalComputer
<F>)
sbrt.kernel.fba.comp.
MsFluxIntervalComputer
<F>
sbrt.kernel.fba.comp.
ReverseRxnIntervalComp
<F>
sbrt.kernel.fba.comp.
SimpleFluxIntervalComputer
<F>
sbrt.kernel.fba.comp.
CdHarFluxComp
<F>
sbrt.kernel.fba.comp.
RxnDeletionComputer
<F>
sbrt.kernel.fba.
AbstractExchangeRxn
(implements sbrt.kernel.fba.
ChemRxn
, sbrt.kernel.fba.
ExchangeRxn
)
sbrt.kernel.fba.
RevExchRxn
sbrt.kernel.fba.
SinkRxn
sbrt.kernel.fba.
SourceRxn
sbrt.kernel.math.
AbstractLinearComb.Term
<V> (implements sbrt.kernel.math.
LinearComb.Term
<V>)
sbrt.kernel.math.
HashLinearComb.Term
<V>
sbrt.shell.text.
AbstractLinkedHashSetFormat
<E> (implements sbrt.shell.text.
LinkedHashSetFormat
<E>)
sbrt.shell.text.
AmpersandSetFormat
<E>
sbrt.shell.text.
PipeSetFormat
<E>
sbrt.shell.text.
TabSetFormat
<E>
sbrt.shell.text.
WhitespaceSetFormat
<E>
sbrt.shell.text.
AbstractListFormat
<E> (implements sbrt.shell.text.
ListFormat
<E>)
sbrt.shell.text.
PipeListFormat
<E>
sbrt.shell.text.
TabListFormat
<E>
sbrt.shell.text.
WhitespaceListFormat
<E>
sbrt.shell.text.
AbstractMapEntryFormat
<K,V> (implements sbrt.shell.text.
MapEntryFormat
<K,V>)
sbrt.shell.text.
ColonMapEntryFormatV1
<K,V>
sbrt.shell.text.
EqualsMapEntryFormatV1
<K,V>
sbrt.shell.text.
AbstractMapFormat
<K,V> (implements sbrt.shell.text.
MapFormat
<K,V>)
sbrt.shell.text.
AppInputFileLineFormatVersion1
(implements sbrt.shell.text.
AppInputFileLineFormat
)
sbrt.shell.text.
ColonMapFormatV1
<K,V>
sbrt.shell.text.fba.
ConstraintsFileLineFormatV1
(implements sbrt.shell.text.fba.
ConstraintsFileLineFormat
<E>)
sbrt.shell.text.fba.
ConstraintsFileLineFormatV2
(implements sbrt.shell.text.fba.
ConstraintsFileLineFormat
<E>)
sbrt.shell.text.
EqualsMapFormatV1
<K,V>
sbrt.shell.text.fba.
FluxCapFormatV1
(implements sbrt.shell.text.fba.
FluxCapFormat
)
sbrt.shell.text.fba.
FluxomeSolFileLineFormatV1
(implements sbrt.shell.text.fba.
FluxomeSolutionFileLineFormat
)
sbrt.shell.text.fba.
FluxVectorFormatV1
(implements sbrt.shell.text.fba.
FluxVectorFormat
)
sbrt.shell.text.fba.
IrfFormatV1
sbrt.shell.text.fba.
MixedFluxomeFormatV1
sbrt.shell.io.
AbstractMapInputFile
<K,V> (implements sbrt.shell.io.
MapTextInputFile
<K,V>)
sbrt.shell.io.
ComiFile
<K,V>
sbrt.shell.io.
RomiFile
<K,V>
sbrt.shell.io.
ProcessInputFile
(implements sbrt.shell.mng.
ManagerInput
<K,V>)
sbrt.shell.io.
AbstractMapOutputFile
<K,V> (implements sbrt.shell.io.
MapTextOutputFile
<K,V>)
sbrt.shell.io.
ComoFile
<K,V>
sbrt.shell.io.
RomoFile
<K,V>
sbrt.kernel.math.algebra.
AbstractMdMatrix
<R,C> (implements sbrt.kernel.math.algebra.
DoubleMatrixBuilder
<R,C>)
sbrt.kernel.math.algebra.
AbstractSmdMatrix
<R,C> (implements sbrt.kernel.math.algebra.
SmdMatrix
<R,C>)
sbrt.kernel.math.algebra.
HashMatrix
<R,C>
sbrt.kernel.math.algebra.
RowOrTreeMatrix
<R,C>
sbrt.kernel.math.algebra.
TreeMatrix
<R,C>
sbrt.kernel.math.
AbstractPolynomial
<V> (implements sbrt.kernel.math.
Polynomial
<V>)
sbrt.kernel.math.
AbstractLinearComb
<V> (implements sbrt.kernel.math.
LinearComb
<V>)
sbrt.kernel.math.
HashLinearComb
<V>
sbrt.shell.mng.
AbstractProcessManager
(implements sbrt.shell.mng.
ProcessManager
<K,V>)
sbrt.shell.mng.fba.
BiggSbmlReaderManager
(implements sbrt.shell.mng.
ShellProcessManager
<K,V>)
sbrt.shell.mng.geom.
CdHarManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.stat.
CorrelationManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.graph_theory.
CycleIdManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.fba.
FbaManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.fba.
CatalystDeletionManager
sbrt.shell.mng.fba.
CvCatalystDeletionManager
sbrt.shell.mng.fba.
CvFbaOptManager
sbrt.shell.mng.fba.
CvMsFluxIntervalManager
sbrt.shell.mng.fba.
CvObjectiveFunctionManager
sbrt.shell.mng.fba.
CvRevRxnFluxIntervalManager
sbrt.shell.mng.fba.
CvRxnDeletionManager
sbrt.shell.mng.fba.
CvSimpleFluxIntervalManager
sbrt.shell.mng.fba.
ExtremeCurrentManager
sbrt.shell.mng.fba.
FbaOptManager
sbrt.shell.mng.fba.
FbaSolverManager
sbrt.shell.mng.fba.
FluxActivityManager
sbrt.shell.mng.fba.
FluxCapManager
sbrt.shell.mng.fba.
FluxPlasticityManager
sbrt.shell.mng.fba.
InitialPointManager
sbrt.shell.mng.fba.
IntervalVariationManager
sbrt.shell.mng.fba.
MsFluxIntervalManager
sbrt.shell.mng.fba.
MsFluxomeReducerManager
sbrt.shell.mng.fba.
NetworkInfoManager
sbrt.shell.mng.fba.
ObjectiveFunctionManager
sbrt.shell.mng.fba.
RandomConstraintsManager
sbrt.shell.mng.fba.
RandomFluxVectorManager
sbrt.shell.mng.fba.
CdHarFluxVectorManager
sbrt.shell.mng.fba.
RandomObjectiveManager
sbrt.shell.mng.fba.
RedundRxnRemoverManager
sbrt.shell.mng.fba.
ReverseRxnFluxIntervalManager
sbrt.shell.mng.fba.
RevRxnBreakerManager
sbrt.shell.mng.fba.
RxnDeletionManager
sbrt.shell.mng.fba.
SimpleFluxIntervalManager
sbrt.shell.mng.fba.
SlpCycleIdManager
sbrt.shell.mng.fba.
WwFluxomeReducerManager
sbrt.shell.mng.graph_theory.
GraphInfoManager
plug_in_example.shell.
GreetingManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.utilities.
IntervalComparisonManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.stat.
KendallTauManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.algebra.
LinearCombConverterManager
(implements sbrt.shell.mng.
ShellProcessManager
<K,V>)
sbrt.shell.mng.algebra.
LinearSolverManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.stat.
MannWhitneyUManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.algebra.
MatrixConverterManager
(implements sbrt.shell.mng.
ShellProcessManager
<K,V>)
sbrt.shell.mng.fba.
MetatoolInputReaderManager
(implements sbrt.shell.mng.
ShellProcessManager
<K,V>)
sbrt.shell.mng.fba.
MetatoolInputWriterManager
(implements sbrt.shell.mng.
ShellProcessManager
<K,V>)
sbrt.shell.mng.fba.
MetatoolOutputReaderManager
(implements sbrt.shell.mng.
ShellProcessManager
<K,V>)
sbrt.shell.mng.algebra.
MultipleVectorsConverterManager
(implements sbrt.shell.mng.
ShellProcessManager
<K,V>)
sbrt.shell.mng.fba.
PalssonSbmlReaderManager
(implements sbrt.shell.mng.
ShellProcessManager
<K,V>)
sbrt.shell.mng.graph_theory.
PathIdManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.fba.
SimpleRxnFileTransManager
(implements sbrt.shell.mng.
ShellProcessManager
<K,V>)
sbrt.shell.mng.comb.
SingleElementUnionManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.algebra.
SingleVectorConverterManager
(implements sbrt.shell.mng.
ShellProcessManager
<K,V>)
sbrt.shell.mng.comb.
StrictSingleElementUnionManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.graph_theory.
UniqueCycleIdManager
(implements sbrt.shell.mng.
ShellProcessManager
<K,V>)
sbrt.shell.mng.utilities.
VariableParticipationManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.shell.mng.utilities.
VectorComparisonManager
(implements sbrt.shell.mng.
KernelProcessManager
<K,V>)
sbrt.kernel.utilities.
AbstractProgressMonitor
(implements sbrt.kernel.utilities.
MutableProgressMonitor
)
sbrt.kernel.utilities.
DiscreteProgressMonitor
sbrt.kernel.utilities.
PercentProgressMonitor
sbrt.kernel.io.
AbstractResultsManager
<R> (implements sbrt.kernel.io.
ResultsManager
<T>)
sbrt.shell.mng.fba.
ExtremeCurrentManager.Rm
sbrt.kernel.io.
ListResultsManager
<R> (implements java.lang.Iterable<T>)
sbrt.kernel.io.
SingleRm
<R>
sbrt.kernel.fba.
AbstractRxn
(implements sbrt.kernel.fba.
ChemRxn
)
sbrt.kernel.fba.
IrrevRxn
sbrt.kernel.fba.
RevRxn
sbrt.shell.io.
AbstractSbrtFile
sbrt.shell.text.fba.
BiggBracketParserV1
sbrt.shell.text.fba.
BiggRxnNodeParser
sbrt.shell.proc.fba.
BiggSbmlReader
sbrt.shell.text.
BoolRelFormatV1
<E> (implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.shell.text.math.
BoundedIntervalFormatV1
(implements sbrt.shell.text.math.
IntervalFormat
)
sbrt.shell.text.chem.
CatalystFormatV1
(implements sbrt.shell.text.chem.
CatalystFormat
)
sbrt.shell.text.chem.
CatalystFormatV2
(implements sbrt.shell.text.chem.
CatalystFormat
)
sbrt.shell.text.fba.
CatalystListFormatV1
(implements sbrt.shell.text.fba.
CatalystListFormat
)
sbrt.shell.text.fba.
CatalystSetFormatV1
(implements sbrt.shell.text.fba.
CatalystSetFormat
)
sbrt.shell.text.fba.
CatalystVerifier
(implements sbrt.shell.text.chem.
CatalystFormat
)
sbrt.kernel.math.geom.comp.
CdHarComp
<V>
sbrt.kernel.math.geom.comp.
CdHarComp.Results
sbrt.kernel.fba.comp.
CdHarFluxComp.Results
sbrt.kernel.math.geom.proc.
CdHarProcess
<V> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.shell.text.chem.
ChemSpeciesFormatV1
(implements sbrt.shell.text.chem.
ChemSpeciesFormat
)
sbrt.shell.text.fba.
ChemSpeciesVerifier
(implements sbrt.shell.text.chem.
ChemSpeciesFormat
)
sbrt.shell.text.math.
CoeffFormatV1
(implements sbrt.shell.text.math.
CoeffFormat
)
sbrt.shell.text.math.
CoeffFormatV2
(implements sbrt.shell.text.math.
CoeffFormat
)
sbrt.shell.io.fba.
CofoofSource
<F> (implements java.util.Iterator<E>)
sbrt.shell.io.fba.
ColumnOrFbaOptOutputFile
<F> (implements sbrt.shell.io.fba.
FbaOptOutputFile
<F>)
sbrt.shell.io.
ComiFileSource
<K,V> (implements java.util.Iterator<E>)
sbrt.shell.io.
ComoFileSource
<K,V> (implements java.util.Iterator<E>)
java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
java.awt.Container
javax.swing.JComponent (implements java.io.Serializable)
javax.swing.JPanel (implements javax.accessibility.Accessible)
sbrt.shell.gui.
TextPaneGui
(implements java.awt.event.ActionListener)
javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
javax.swing.JEditorPane
javax.swing.JTextPane
sbrt.shell.gui.
SbrtOutputPane
sbrt.kernel.math.stat.proc.
CorrelationAnalysis
<V,T> (implements sbrt.kernel.
KernelProcess
<T>)
sbrt.shell.text.math.
CorrResFormatterV1
(implements sbrt.shell.text.math.
CorrResultsFormatter
<T>)
sbrt.ext.cplex.
CplexSolver
<R,C> (implements sbrt.kernel.math.optimization.
LinearProgramSolver
<R,C>, sbrt.kernel.math.optimization.
QuadraticProgramSolver
<R,C>)
sbrt.kernel.math.graph_theory.proc.
CycleIdProcess
<N> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.math.graph_theory.
DirectedGraph
<N>
sbrt.kernel.math.graph_theory.
DirectedGraph.Edge
<N>
sbrt.shell.text.math.
DirEdgeFormatV1
<N> (implements sbrt.shell.text.math.
DirEdgeFormat
<N>)
sbrt.kernel.math.
DoubleEquiv
(implements sbrt.kernel.math.
EquivTester
<T>)
sbrt.shell.text.
DoubleFormatV1
(implements sbrt.shell.text.
DoubleFormat
)
sbrt.shell.text.
DoubleFormatV2
(implements sbrt.shell.text.
DoubleFormat
)
sbrt.ext.R.
DummyConsole
(implements org.rosuda.JRI.RMainLoopCallbacks)
sbrt.shell.io.
EndOfFile
(implements java.io.Serializable)
sbrt.kernel.math.geom.comp.
EuclideanDist
sbrt.shell.text.fba.
FbaOptFileLineFormatV1
(implements sbrt.shell.text.fba.
FbaOptFileLineFormat
)
sbrt.shell.text.fba.
FbaOptHeaderFormatterV1
(implements sbrt.shell.text.fba.
FbaOptHeaderFormatter
)
sbrt.shell.text.fba.
FbaOptHeaderParserV1
(implements sbrt.shell.text.fba.
FbaOptHeaderParser
)
sbrt.kernel.fba.comp.
FbaOptimizer
<F> (implements sbrt.kernel.fba.comp.
FluxCvComputer
<F>)
sbrt.kernel.fba.comp.
FbaOptimizer.Results
sbrt.kernel.fba.proc.
FbaProcess
<F,R> (implements sbrt.kernel.
KernelProcess
<T>)
sbrt.kernel.fba.proc.
AbstractCvFbaOptProcess
<F,R>
sbrt.kernel.fba.proc.
CvFluxIntervalProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
SvCdHarFluxVectorProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
SvInitialPointProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
CatalystDeletionProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
CdHarFluxVectorProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
CvCatalystDeletionProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
CvFbaOptProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
CvObjectiveFunctionProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
CvRxnDeletionProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
CycleIdProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
ExtremeCurrentProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
FbaOptProcess
<F>
sbrt.kernel.fba.proc.
FbaSolverProcess
<F>
sbrt.kernel.fba.proc.
FluxActivityProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
FluxCapProcess
(implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
FluxIntervalProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
FluxomeReducerProcess
<T> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
FluxPlasticityProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
InitialPointGenerator
<F>
sbrt.kernel.fba.proc.
NetworkInfoProcess
<F>
sbrt.kernel.fba.proc.
ObjFunAnalysis
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
RandConstGeneratorV1
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
RandomObjectiveGenerator
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.proc.
RedundRxnRemoverProcess
sbrt.kernel.fba.proc.
RxnDeletionProcess
<F> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.fba.comp.
FbaSolver
sbrt.shell.io.
FileFormat
sbrt.shell.text.
FileFormatFormat
(implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.shell.io.
FileLineIterator
<E> (implements java.util.Iterator<E>)
sbrt.shell.io.
SerializedFileIterator
<E>
sbrt.shell.io.
TextFileLineIterator
<E>
sbrt.kernel.fba.proc.
FluxActivityProcess.Results
sbrt.kernel.fba.comp.
FluxCapComputer
sbrt.shell.io.fba.
FluxCapInputFile
(implements sbrt.shell.io.
MapTextInputFile
<K,V>)
sbrt.kernel.fba.
FluxConstraints
sbrt.kernel.fba.analysis.
FluxIntervalAnalyzer
sbrt.shell.io.fba.
FluxIntervalInputFile
(implements sbrt.shell.io.
InputFile
<E>)
sbrt.kernel.fba.proc.
FluxPlasticityProcess.Results
sbrt.ext.glpk.
GlpkSolver
<R,C> (implements sbrt.kernel.math.optimization.
LinearProgramSolver
<R,C>)
plug_in_example.kernel.
GreetingProcess
(implements sbrt.kernel.
KernelProcess
<T>)
sbrt.kernel.math.geom.comp.
Hamming
sbrt.kernel.math.geom.
HashConvexPolytope
<V> (implements sbrt.kernel.math.geom.
ConvexPolytope
<V>)
sbrt.kernel.math.algebra.
HashLinearSystemSolution
<V> (implements sbrt.kernel.math.algebra.
LinearSystemSolution
<V>)
sbrt.shell.
HomeDirectory
sbrt.kernel.math.algebra.
IndexPair
<R,C>
sbrt.shell.text.math.
IndexPairFormatV1
<R,C> (implements sbrt.shell.text.math.
IndexPairFormat
<R,C>)
sbrt.kernel.fba.comp.
InitialPointComputer
<F> (implements sbrt.kernel.fba.comp.
FluxCvComputer
<F>)
sbrt.kernel.fba.comp.
InitialPointComputer.Results
sbrt.shell.text.
IntegerFormatV1
(implements sbrt.shell.text.
IntegerFormat
)
sbrt.kernel.math.
Interval
(implements java.io.Serializable)
sbrt.kernel.math.
IntervalComparer
sbrt.kernel.math.
IntervalComparer.Diff
<V>
sbrt.kernel.utilities.proc.
IntervalComparison
<V> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.math.
IntervalEquiv
(implements sbrt.kernel.math.
EquivTester
<T>)
sbrt.shell.text.math.
IntervalFormatV1
(implements sbrt.shell.text.math.
IntervalFormat
)
sbrt.kernel.fba.
IrrevRxnFluxomeV1
(implements sbrt.kernel.fba.
IrrevRxnFluxome
)
sbrt.shell.text.chem.
IrrevRxnFormatV1
(implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.shell.text.fba.
IrrevRxnFormatV1
(implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.shell.text.fba.
IrrevRxnFormatV2
(implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.kernel.math.stat.comp.
KendallTau
<V> (implements sbrt.kernel.math.stat.comp.
Correlator
<V,T>)
sbrt.kernel.math.stat.comp.
KendallTauA
<V>
sbrt.kernel.math.stat.comp.
KendallTauB
<V>
sbrt.shell.text.math.
LinCombTermFormatV1
<V> (implements sbrt.shell.text.math.
LinearCombTermFormat
<V>)
sbrt.shell.text.math.
LinCombTermFormatV2
<V> (implements sbrt.shell.text.math.
LinearCombTermFormat
<V>)
sbrt.shell.text.math.
LinearCombFormatV1
<V> (implements sbrt.shell.text.math.
LinearCombFormat
<V>)
sbrt.shell.text.math.
LinearCombFormatV2
<V> (implements sbrt.shell.text.math.
LinearCombFormat
<V>)
sbrt.kernel.math.algebra.proc.
LinearSolverProcess
<V> (implements sbrt.kernel.
KernelProcess
<T>)
sbrt.kernel.utilities.
LogicalRelation
<C> (implements java.lang.Iterable<T>)
sbrt.kernel.utilities.
And
<C>
sbrt.kernel.utilities.
Or
<C>
sbrt.shell.text.
LongFormatV1
(implements sbrt.shell.text.
LongFormat
)
sbrt.kernel.math.stat.comp.
MannWhitneyResults
sbrt.kernel.math.stat.comp.
MannWhitneyU
sbrt.shell.mng.
MapManagerInput
<K,V> (implements sbrt.shell.mng.
ManagerInput
<K,V>)
sbrt.ext.mma.algebra.
MathematicaSolver
<V> (implements sbrt.kernel.math.algebra.
LinearSystemSolver
<V>)
sbrt.kernel.math.algebra.
MatrixElement
<R,C,E>
sbrt.shell.text.math.
MatrixElementFormatV1
<R,C> (implements sbrt.shell.text.math.
MatrixElementFormat
<R,C,E>)
sbrt.kernel.math.algebra.
MatrixMultiplier
sbrt.kernel.math.algebra.
MatrixTransposer
sbrt.kernel.math.algebra.
MatrixWrap
<R,C,E> (implements sbrt.kernel.math.algebra.
Matrix
<R,C,E>)
sbrt.kernel.math.algebra.
DoubleMatrixWrap
<R,C> (implements sbrt.kernel.math.algebra.
DoubleMatrix
<R,C>)
sbrt.kernel.math.algebra.
SparseDoubleMatrixWrap
<R,C> (implements sbrt.kernel.math.algebra.
SparseDoubleMatrix
<R,C>)
sbrt.shell.proc.fba.
MetatoolInputReader
sbrt.shell.proc.fba.
MetatoolInputReader.Results
sbrt.shell.proc.fba.
MetatoolInputWriter
sbrt.shell.proc.fba.
MetatoolOutputReader
sbrt.kernel.fba.
MixedFluxomeV1
(implements sbrt.kernel.fba.
MixedFluxome
)
sbrt.ext.mma.algebra.
MMaExprInterpretter
sbrt.kernel.fba.comp.
MsFluxomeReducer
(implements sbrt.kernel.fba.comp.
FluxomeReducer
<T>)
sbrt.shell.io.
MultiOutputFiles
<F,R> (implements sbrt.kernel.io.
ResultsManager
<T>)
sbrt.kernel.math.stat.proc.
MultipleCorrelationAnalysis
<V,T> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.math.stat.proc.
MwUAnalysis
<V> (implements sbrt.kernel.
KernelProcess
<T>)
sbrt.kernel.fba.proc.
NetworkInfoProcess.Results
<F>
sbrt.shell.text.
NonEmptyStringFormat
(implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.kernel.math.stat.
NormalDist
java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
java.io.FilterOutputStream
java.io.PrintStream (implements java.lang.Appendable, java.io.Closeable)
sbrt.shell.io.
DevNull
sbrt.shell.gui.
TextAreaOutputStream
sbrt.shell.gui.
TextPaneOutputStream
sbrt.shell.text.fba.
PalssonRxnNodeParser
sbrt.shell.proc.fba.
PalssonSbmlReader
sbrt.kernel.math.geom.
ParallelHyperplanes
<V>
sbrt.kernel.math.graph_theory.
Path
<N>
sbrt.kernel.math.graph_theory.comp.
PathFinder
<N>
sbrt.kernel.math.graph_theory.proc.
PathIdProcess
<N> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.shell.text.
PercentFormatVersion1
(implements sbrt.shell.text.
PercentFormat
)
sbrt.shell.
ProcessManagerFactory
sbrt.
ProcessRunner
sbrt.shell.
ProgramSolverFactory
sbrt.ext.R.
R
sbrt.ext.R.stat.
RCorrelator
<V> (implements sbrt.kernel.math.stat.comp.
Correlator
<V,T>)
sbrt.ext.R.stat.
RKendall
<V>
sbrt.ext.R.stat.
RPearson
<V>
sbrt.ext.R.stat.
RSpearman
<V>
sbrt.ext.R.stat.
RCorrelator.Result
(implements sbrt.kernel.math.stat.comp.
CorrResult
)
sbrt.kernel.fba.comp.
RedundRxnRemover
sbrt.kernel.fba.proc.
RevRxnBreakerProcess
(implements sbrt.kernel.
KernelProcess
<T>)
sbrt.shell.text.chem.
RevRxnFormatV1
(implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.shell.text.fba.
RevRxnFormatV1
(implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.shell.text.fba.
RevRxnFormatV2
(implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.shell.io.fba.
RofoofSource
<F> (implements java.util.Iterator<E>)
sbrt.shell.io.
RomiFileSource
<K,V> (implements java.util.Iterator<E>)
sbrt.shell.io.
RomoFileSource
<K,V> (implements java.util.Iterator<E>)
sbrt.shell.io.fba.
RowOrFbaOptOutputFile
<F> (implements sbrt.shell.io.fba.
FbaOptOutputFile
<F>)
sbrt.kernel.fba.
RxnComparer
sbrt.shell.text.fba.
RxnFormatV1
(implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.shell.text.fba.
RxnNameExprFormatV1
(implements sbrt.shell.text.fba.
RxnNameExprFormat
<E,S>)
sbrt.shell.text.chem.
RxnNameFormatV1
(implements sbrt.shell.text.chem.
RxnNameFormat
<T>)
sbrt.shell.text.fba.
RxnNameListFormatV1
(implements sbrt.shell.text.fba.
RxnNameListFormat
)
sbrt.shell.text.fba.
RxnNameOrExprFormatV1
(implements sbrt.shell.text.fba.
RxnNameOrExprFormat
)
sbrt.shell.text.fba.
RxnNameSetFormatV1
(implements sbrt.shell.text.fba.
RxnNameSetFormat
)
sbrt.shell.text.fba.
RxnNameVerifier
(implements sbrt.shell.text.chem.
RxnNameFormat
<T>)
sbrt.
Sbrt
sbrt.shell.text.math.
SenseFormat
(implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.shell.io.fba.
SerFbaOptOutputFile
<F> (implements sbrt.shell.io.fba.
FbaOptOutputFile
<F>)
sbrt.shell.io.
SerializedInputFile
<E> (implements sbrt.shell.io.
InputFile
<E>)
sbrt.shell.io.
SerializedMapInputFile
<K,V> (implements sbrt.shell.io.
MapInputFile
<K,V>)
sbrt.shell.io.
SerializedOutputFile
<E> (implements sbrt.shell.io.
OutputFile
<T>)
sbrt.shell.io.
SmoFile
<K,V> (implements sbrt.shell.io.
MapOutputFile
<K,V>)
sbrt.shell.io.fba.
SfoofSource
<F> (implements java.util.Iterator<E>)
sbrt.shell.text.
SimpleListFormat
<E> (implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.shell.proc.fba.
SimpleRxnFileReader
sbrt.shell.text.
SimpleSetFormat
<E> (implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.kernel.math.comb.proc.
SingleElementUnionProc
<E> (implements sbrt.kernel.
KernelProcess
<T>)
sbrt.kernel.math.comb.comp.
SingleElementUnionsV1
sbrt.kernel.math.comb.comp.
SingleElementUnionsV2
sbrt.kernel.fba.comp.
SlpCycleComputer
(implements sbrt.kernel.fba.comp.
CycleComputer
<F>)
sbrt.kernel.fba.comp.
SlpExCurrComputerV2
(implements sbrt.kernel.fba.comp.
ExtremeCurrentComputer
)
sbrt.shell.io.
SmoFileSource
<K,V> (implements java.util.Iterator<E>)
sbrt.shell.text.
SpecialChars
sbrt.kernel.math.comb.proc.
StrictSingleElementUnionProc
<E> (implements sbrt.kernel.
KernelProcess
<T>)
sbrt.kernel.math.comb.comp.
StrictSingleElementUnions
sbrt.shell.text.
StringFormat
(implements sbrt.shell.text.
SimpleFormat
<T>)
sbrt.kernel.math.stat.comp.
TauResult
(implements sbrt.kernel.math.stat.comp.
CorrResult
)
sbrt.kernel.math.geom.comp.
Taxicab
sbrt.shell.io.
TextInputFile
<E> (implements sbrt.shell.io.
InputFile
<E>)
sbrt.shell.io.fba.
RxnNamExprSetInputFile
<E,S>
sbrt.shell.io.
TextOutputFile
<T> (implements sbrt.shell.io.
OutputFile
<T>)
java.lang.Throwable (implements java.io.Serializable)
java.lang.Exception
java.lang.RuntimeException
sbrt.shell.
ApplicationException
sbrt.shell.text.
FormatException
sbrt.kernel.io.
ConflictingInputException
sbrt.kernel.math.
ConstraintViolationException
sbrt.kernel.math.geom.
DimensionException
sbrt.kernel.math.
ExceededLimitException
sbrt.ext.
ExternalSoftwareException
sbrt.ext.mma.
MathematicaException
sbrt.kernel.math.optimization.
ProgramSolverException
sbrt.
FatalException
sbrt.kernel.fba.comp.
FbaOptException
sbrt.kernel.fba.comp.
FluxCapException
sbrt.kernel.fba.comp.
FluxRangeException
sbrt.kernel.math.
IllegalBoundsException
sbrt.kernel.math.algebra.
IllegalFreeVariableException
sbrt.kernel.math.
InfeasibleSolutionException
sbrt.kernel.fba.comp.
InvalidFluxVectorException
sbrt.kernel.math.
InvalidPointException
sbrt.ext.R.
JriException
sbrt.kernel.math.
MissingVariableException
sbrt.kernel.math.
UnboundedVariableException
sbrt.shell.text.
TrueFalseFormat
(implements sbrt.shell.text.
BooleanFormat
)
sbrt.kernel.utilities.
UnmodifiableCollection
<E> (implements java.util.Collection<E>)
sbrt.kernel.utilities.
UnmodifiableIterator
<E> (implements java.util.Iterator<E>)
sbrt.kernel.utilities.
UnmodifiableList
<E> (implements java.util.List<E>)
sbrt.kernel.utilities.
UnmodifiableMap
<K,V> (implements java.util.Map<K,V>)
sbrt.kernel.utilities.
UnmodifiableSet
<E> (implements java.util.Set<E>)
sbrt.kernel.utilities.
Util
sbrt.kernel.utilities.proc.
VariableParticipation
<E,V> (implements sbrt.kernel.
KernelProcess
<T>)
sbrt.kernel.math.
VectorComparer
sbrt.kernel.math.
VectorComparer.Diff
<V>
sbrt.kernel.utilities.proc.
VectorComparison
<V> (implements sbrt.kernel.
MonitoredProcess
<R>)
sbrt.kernel.math.algebra.proc.
VectorIntersection
<K,V> (implements sbrt.kernel.
KernelProcess
<T>)
sbrt.kernel.io.
WarningHandlerFactory
sbrt.shell.
WorkingDirectory
sbrt.kernel.fba.comp.
WwFluxomeReducer
(implements sbrt.kernel.fba.comp.
FluxomeReducer
<T>)
sbrt.shell.io.
XmlFileFactory
sbrt.shell.text.
YesNoFormat
(implements sbrt.shell.text.
BooleanFormat
)
Interface Hierarchy
sbrt.kernel.fba.
ChemRxn
sbrt.kernel.fba.
ExchangeRxn
sbrt.kernel.math.geom.
ConvexPolytope
<V>
sbrt.kernel.math.stat.comp.
Correlator
<V,T>
sbrt.kernel.math.stat.comp.
CorrResult
sbrt.kernel.fba.comp.
CycleComputer
<F>
sbrt.kernel.math.
EquivTester
<T>
sbrt.kernel.fba.comp.
ExtremeCurrentComputer
sbrt.kernel.fba.comp.
FluxCvComputer
<F>
sbrt.kernel.fba.comp.
FluxIntervalComputer
<F>
sbrt.kernel.fba.
Fluxome
sbrt.kernel.fba.
CatalyzedFluxome
sbrt.kernel.fba.
IrrevRxnFluxome
sbrt.kernel.fba.
MixedFluxome
sbrt.kernel.fba.
IrrevRxnFluxome
sbrt.kernel.fba.
MixedFluxome
sbrt.kernel.fba.comp.
FluxomeReducer
<T>
sbrt.shell.text.
Format
sbrt.shell.text.
AppInputFileLineFormat
sbrt.shell.text.
BooleanFormat
sbrt.shell.text.chem.
CatalystFormat
sbrt.shell.text.fba.
CatalystListFormat
sbrt.shell.text.fba.
CatalystSetFormat
sbrt.shell.text.chem.
ChemSpeciesFormat
sbrt.shell.text.math.
CoeffFormat
sbrt.shell.text.
CollectionFormat
<E>
sbrt.shell.text.fba.
ConstraintsFileLineFormat
<E>
sbrt.shell.text.math.
DirEdgeFormat
<N>
sbrt.shell.text.
DoubleFormat
sbrt.shell.text.fba.
FbaOptFileLineFormat
sbrt.shell.text.fba.
FluxCapFormat
sbrt.shell.text.fba.
FluxomeSolutionFileLineFormat
sbrt.shell.text.fba.
FluxVectorFormat
sbrt.shell.text.math.
IndexPairFormat
<R,C>
sbrt.shell.text.
IntegerFormat
sbrt.shell.text.math.
IntervalFormat
sbrt.shell.text.math.
LinearCombFormat
<V>
sbrt.shell.text.math.
LinearCombTermFormat
<V>
sbrt.shell.text.
LongFormat
sbrt.shell.text.
MapEntryFormat
<K,V>
sbrt.shell.text.
MapFormat
<K,V>
sbrt.shell.text.
AppInputFileLineFormat
sbrt.shell.text.fba.
ConstraintsFileLineFormat
<E>
sbrt.shell.text.fba.
FbaOptFileLineFormat
sbrt.shell.text.fba.
FluxCapFormat
sbrt.shell.text.fba.
FluxomeSolutionFileLineFormat
sbrt.shell.text.fba.
FluxVectorFormat
sbrt.shell.text.math.
MathExprFormat
<E,V>
sbrt.shell.text.math.
LinearCombFormat
<V>
sbrt.shell.text.math.
MatrixElementFormat
<R,C,E>
sbrt.shell.text.
PercentFormat
sbrt.shell.text.fba.
RxnNameExprFormat
<E,S>
sbrt.shell.text.chem.
RxnNameFormat
<T>
sbrt.shell.text.fba.
RxnNameListFormat
sbrt.shell.text.fba.
RxnNameOrExprFormat
sbrt.shell.text.fba.
RxnNameSetFormat
sbrt.shell.text.
SimpleFormat
<T> (also extends sbrt.shell.text.
Formatter
<T>, sbrt.shell.text.
Parser
<T>)
sbrt.shell.text.
BooleanFormat
sbrt.shell.text.chem.
CatalystFormat
sbrt.shell.text.fba.
CatalystListFormat
sbrt.shell.text.fba.
CatalystSetFormat
sbrt.shell.text.chem.
ChemSpeciesFormat
sbrt.shell.text.math.
CoeffFormat
sbrt.shell.text.
CollectionFormat
<E>
sbrt.shell.text.math.
DirEdgeFormat
<N>
sbrt.shell.text.
DoubleFormat
sbrt.shell.text.math.
IndexPairFormat
<R,C>
sbrt.shell.text.
IntegerFormat
sbrt.shell.text.math.
IntervalFormat
sbrt.shell.text.math.
LinearCombFormat
<V>
sbrt.shell.text.math.
LinearCombTermFormat
<V>
sbrt.shell.text.
LongFormat
sbrt.shell.text.math.
MathExprFormat
<E,V>
sbrt.shell.text.math.
LinearCombFormat
<V>
sbrt.shell.text.math.
MatrixElementFormat
<R,C,E>
sbrt.shell.text.
PercentFormat
sbrt.shell.text.fba.
RxnNameExprFormat
<E,S>
sbrt.shell.text.chem.
RxnNameFormat
<T>
sbrt.shell.text.fba.
RxnNameListFormat
sbrt.shell.text.fba.
RxnNameOrExprFormat
sbrt.shell.text.fba.
RxnNameSetFormat
sbrt.shell.text.
Formatter
<T>
sbrt.shell.text.
BooleanFormat
sbrt.shell.text.chem.
CatalystFormat
sbrt.shell.text.fba.
CatalystListFormat
sbrt.shell.text.fba.
CatalystSetFormat
sbrt.shell.text.chem.
ChemSpeciesFormat
sbrt.shell.text.math.
CoeffFormat
sbrt.shell.text.
CollectionFormat
<E>
sbrt.shell.text.math.
CorrResultsFormatter
<T>
sbrt.shell.text.math.
DirEdgeFormat
<N>
sbrt.shell.text.
DoubleFormat
sbrt.shell.text.fba.
FbaOptHeaderFormatter
sbrt.shell.text.math.
IndexPairFormat
<R,C>
sbrt.shell.text.
IntegerFormat
sbrt.shell.text.math.
IntervalFormat
sbrt.shell.text.math.
LinearCombFormat
<V>
sbrt.shell.text.math.
LinearCombTermFormat
<V>
sbrt.shell.text.
LinkedHashSetFormat
<E> (also extends sbrt.shell.text.
Parser
<T>)
sbrt.shell.text.
ListFormat
<E> (also extends sbrt.shell.text.
Parser
<T>)
sbrt.shell.text.
LongFormat
sbrt.shell.text.math.
MathExprFormat
<E,V>
sbrt.shell.text.math.
LinearCombFormat
<V>
sbrt.shell.text.math.
MatrixElementFormat
<R,C,E>
sbrt.shell.text.
PercentFormat
sbrt.shell.text.fba.
RxnNameExprFormat
<E,S>
sbrt.shell.text.chem.
RxnNameFormat
<T>
sbrt.shell.text.fba.
RxnNameListFormat
sbrt.shell.text.fba.
RxnNameOrExprFormat
sbrt.shell.text.fba.
RxnNameSetFormat
sbrt.shell.text.
SimpleFormat
<T> (also extends sbrt.shell.text.
Format
, sbrt.shell.text.
Parser
<T>)
sbrt.shell.text.
BooleanFormat
sbrt.shell.text.chem.
CatalystFormat
sbrt.shell.text.fba.
CatalystListFormat
sbrt.shell.text.fba.
CatalystSetFormat
sbrt.shell.text.chem.
ChemSpeciesFormat
sbrt.shell.text.math.
CoeffFormat
sbrt.shell.text.
CollectionFormat
<E>
sbrt.shell.text.math.
DirEdgeFormat
<N>
sbrt.shell.text.
DoubleFormat
sbrt.shell.text.math.
IndexPairFormat
<R,C>
sbrt.shell.text.
IntegerFormat
sbrt.shell.text.math.
IntervalFormat
sbrt.shell.text.math.
LinearCombFormat
<V>
sbrt.shell.text.math.
LinearCombTermFormat
<V>
sbrt.shell.text.
LongFormat
sbrt.shell.text.math.
MathExprFormat
<E,V>
sbrt.shell.text.math.
LinearCombFormat
<V>
sbrt.shell.text.math.
MatrixElementFormat
<R,C,E>
sbrt.shell.text.
PercentFormat
sbrt.shell.text.fba.
RxnNameExprFormat
<E,S>
sbrt.shell.text.chem.
RxnNameFormat
<T>
sbrt.shell.text.fba.
RxnNameListFormat
sbrt.shell.text.fba.
RxnNameOrExprFormat
sbrt.shell.text.fba.
RxnNameSetFormat
java.lang.Iterable<T>
sbrt.shell.io.
InputFile
<E> (also extends sbrt.shell.io.
SbrtFile
)
sbrt.shell.io.
MapInputFile
<K,V>
sbrt.shell.io.
MapTextInputFile
<K,V> (also extends sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
MapTextInputFile
<K,V> (also extends sbrt.shell.io.
MapInputFile
<K,V>, sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.kernel.math.
LinearComb
<V> (also extends sbrt.kernel.math.
Polynomial
<V>)
sbrt.kernel.math.
LinearComb.Term
<V>
sbrt.shell.io.
MapInputFile
<K,V>
sbrt.shell.io.
MapTextInputFile
<K,V> (also extends sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
MapTextInputFile
<K,V> (also extends sbrt.shell.io.
MapInputFile
<K,V>, sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.kernel.math.
Polynomial.Term
<V>
sbrt.kernel.math.
LinearComb.Term
<V>
sbrt.kernel.math.
QuadraticExpr.Term
<V>
sbrt.kernel.math.
QuadraticExpr.Term
<V>
sbrt.kernel.
KernelProcess
<T>
sbrt.kernel.
MonitoredProcess
<R>
sbrt.kernel.math.algebra.
LinearSystemSolution
<V>
sbrt.kernel.math.algebra.
LinearSystemSolver
<V>
sbrt.shell.mng.
ManagerInput
<K,V>
sbrt.kernel.math.
MathExpr
<V>
sbrt.kernel.math.
LinearComb
<V> (also extends java.lang.Iterable<T>, sbrt.kernel.math.
Polynomial
<V>)
sbrt.kernel.math.
Polynomial
<V>
sbrt.kernel.math.
LinearComb
<V> (also extends java.lang.Iterable<T>)
sbrt.kernel.math.
QuadraticExpr
<V>
sbrt.kernel.math.
QuadraticExpr
<V>
sbrt.kernel.math.algebra.
Matrix
<R,C,E>
sbrt.kernel.math.algebra.
DoubleMatrix
<R,C>
sbrt.kernel.math.algebra.
DoubleMatrixBuilder
<R,C> (also extends sbrt.kernel.math.algebra.
MatrixBuilder
<R,C,E>)
sbrt.kernel.math.algebra.
SmdMatrix
<R,C> (also extends sbrt.kernel.math.algebra.
SparseDoubleMatrix
<R,C>)
sbrt.kernel.math.algebra.
SmdMatrix
<R,C> (also extends sbrt.kernel.math.algebra.
DoubleMatrixBuilder
<R,C>, sbrt.kernel.math.algebra.
SparseDoubleMatrix
<R,C>)
sbrt.kernel.math.algebra.
SparseDoubleMatrix
<R,C>
sbrt.kernel.math.algebra.
SmdMatrix
<R,C> (also extends sbrt.kernel.math.algebra.
DoubleMatrixBuilder
<R,C>)
sbrt.kernel.math.algebra.
DoubleMatrixBuilder
<R,C> (also extends sbrt.kernel.math.algebra.
DoubleMatrix
<R,C>, sbrt.kernel.math.algebra.
MatrixBuilder
<R,C,E>)
sbrt.kernel.math.algebra.
SmdMatrix
<R,C> (also extends sbrt.kernel.math.algebra.
SparseDoubleMatrix
<R,C>)
sbrt.kernel.math.algebra.
MatrixBuilder
<R,C,E>
sbrt.kernel.math.algebra.
DoubleMatrixBuilder
<R,C> (also extends sbrt.kernel.math.algebra.
DoubleMatrix
<R,C>)
sbrt.kernel.math.algebra.
SmdMatrix
<R,C> (also extends sbrt.kernel.math.algebra.
SparseDoubleMatrix
<R,C>)
sbrt.kernel.math.algebra.
SmdMatrix
<R,C> (also extends sbrt.kernel.math.algebra.
DoubleMatrixBuilder
<R,C>, sbrt.kernel.math.algebra.
SparseDoubleMatrix
<R,C>)
sbrt.kernel.math.algebra.
SmdMatrix
<R,C> (also extends sbrt.kernel.math.algebra.
DoubleMatrixBuilder
<R,C>, sbrt.kernel.math.algebra.
SparseDoubleMatrix
<R,C>)
sbrt.kernel.math.algebra.
SparseDoubleMatrix
<R,C>
sbrt.kernel.math.algebra.
SmdMatrix
<R,C> (also extends sbrt.kernel.math.algebra.
DoubleMatrixBuilder
<R,C>)
sbrt.shell.text.
Parser
<T>
sbrt.shell.text.
BooleanFormat
sbrt.shell.text.chem.
CatalystFormat
sbrt.shell.text.fba.
CatalystListFormat
sbrt.shell.text.fba.
CatalystSetFormat
sbrt.shell.text.chem.
ChemSpeciesFormat
sbrt.shell.text.math.
CoeffFormat
sbrt.shell.text.
CollectionFormat
<E>
sbrt.shell.text.math.
DirEdgeFormat
<N>
sbrt.shell.text.
DoubleFormat
sbrt.shell.text.fba.
FbaOptHeaderParser
sbrt.shell.text.math.
IndexPairFormat
<R,C>
sbrt.shell.text.
IntegerFormat
sbrt.shell.text.math.
IntervalFormat
sbrt.shell.text.math.
LinearCombFormat
<V>
sbrt.shell.text.math.
LinearCombTermFormat
<V>
sbrt.shell.text.
LinkedHashSetFormat
<E> (also extends sbrt.shell.text.
Formatter
<T>)
sbrt.shell.text.
ListFormat
<E> (also extends sbrt.shell.text.
Formatter
<T>)
sbrt.shell.text.
LongFormat
sbrt.shell.text.math.
MathExprFormat
<E,V>
sbrt.shell.text.math.
LinearCombFormat
<V>
sbrt.shell.text.math.
MatrixElementFormat
<R,C,E>
sbrt.shell.text.
PercentFormat
sbrt.shell.text.fba.
RxnNameExprFormat
<E,S>
sbrt.shell.text.chem.
RxnNameFormat
<T>
sbrt.shell.text.fba.
RxnNameListFormat
sbrt.shell.text.fba.
RxnNameOrExprFormat
sbrt.shell.text.fba.
RxnNameSetFormat
sbrt.shell.text.
SimpleFormat
<T> (also extends sbrt.shell.text.
Format
, sbrt.shell.text.
Formatter
<T>)
sbrt.shell.text.
BooleanFormat
sbrt.shell.text.chem.
CatalystFormat
sbrt.shell.text.fba.
CatalystListFormat
sbrt.shell.text.fba.
CatalystSetFormat
sbrt.shell.text.chem.
ChemSpeciesFormat
sbrt.shell.text.math.
CoeffFormat
sbrt.shell.text.
CollectionFormat
<E>
sbrt.shell.text.math.
DirEdgeFormat
<N>
sbrt.shell.text.
DoubleFormat
sbrt.shell.text.math.
IndexPairFormat
<R,C>
sbrt.shell.text.
IntegerFormat
sbrt.shell.text.math.
IntervalFormat
sbrt.shell.text.math.
LinearCombFormat
<V>
sbrt.shell.text.math.
LinearCombTermFormat
<V>
sbrt.shell.text.
LongFormat
sbrt.shell.text.math.
MathExprFormat
<E,V>
sbrt.shell.text.math.
LinearCombFormat
<V>
sbrt.shell.text.math.
MatrixElementFormat
<R,C,E>
sbrt.shell.text.
PercentFormat
sbrt.shell.text.fba.
RxnNameExprFormat
<E,S>
sbrt.shell.text.chem.
RxnNameFormat
<T>
sbrt.shell.text.fba.
RxnNameListFormat
sbrt.shell.text.fba.
RxnNameOrExprFormat
sbrt.shell.text.fba.
RxnNameSetFormat
sbrt.shell.mng.
ProcessManager
<K,V>
sbrt.shell.mng.
KernelProcessManager
<K,V>
sbrt.shell.mng.
ShellProcessManager
<K,V>
sbrt.kernel.math.optimization.
ProgramSolver
<R,C>
sbrt.kernel.math.optimization.
LinearProgramSolver
<R,C>
sbrt.kernel.math.optimization.
QuadraticProgramSolver
<R,C>
sbrt.kernel.utilities.
ProgressMonitor
sbrt.kernel.utilities.
MutableProgressMonitor
sbrt.kernel.io.
ResultsManager
<T>
sbrt.shell.io.fba.
FbaOptOutputFile
<F>
sbrt.shell.io.
MapOutputFile
<K,V>
sbrt.shell.io.
MapTextOutputFile
<K,V> (also extends sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
MapTextOutputFile
<K,V> (also extends sbrt.shell.io.
MapOutputFile
<K,V>, sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
OutputFile
<T> (also extends sbrt.shell.io.
SbrtFile
)
sbrt.shell.io.fba.
FbaOptOutputFile
<F>
sbrt.shell.io.
MapOutputFile
<K,V>
sbrt.shell.io.
MapTextOutputFile
<K,V> (also extends sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
MapTextOutputFile
<K,V> (also extends sbrt.shell.io.
MapOutputFile
<K,V>, sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
SbrtFile
sbrt.shell.io.fba.
FbaOptOutputFile
<F>
sbrt.shell.io.
InputFile
<E> (also extends java.lang.Iterable<T>)
sbrt.shell.io.
MapInputFile
<K,V>
sbrt.shell.io.
MapTextInputFile
<K,V> (also extends sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
MapTextInputFile
<K,V> (also extends sbrt.shell.io.
MapInputFile
<K,V>, sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
MapInputFile
<K,V>
sbrt.shell.io.
MapTextInputFile
<K,V> (also extends sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
MapOutputFile
<K,V>
sbrt.shell.io.
MapTextOutputFile
<K,V> (also extends sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
MapTextFile
<K,V>
sbrt.shell.io.
MapTextInputFile
<K,V> (also extends sbrt.shell.io.
MapInputFile
<K,V>)
sbrt.shell.io.
MapTextOutputFile
<K,V> (also extends sbrt.shell.io.
MapOutputFile
<K,V>)
sbrt.shell.io.
MapTextInputFile
<K,V> (also extends sbrt.shell.io.
MapInputFile
<K,V>, sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
MapTextOutputFile
<K,V> (also extends sbrt.shell.io.
MapOutputFile
<K,V>, sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
OutputFile
<T> (also extends sbrt.kernel.io.
ResultsManager
<T>)
sbrt.shell.io.fba.
FbaOptOutputFile
<F>
sbrt.shell.io.
MapOutputFile
<K,V>
sbrt.shell.io.
MapTextOutputFile
<K,V> (also extends sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.shell.io.
MapTextOutputFile
<K,V> (also extends sbrt.shell.io.
MapOutputFile
<K,V>, sbrt.shell.io.
MapTextFile
<K,V>)
sbrt.kernel.io.
WarningHandler
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
sbrt.kernel.math.optimization.
OptSense
sbrt.kernel.math.optimization.
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