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