A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

O

OBJ_FUNCT_FILE - Static variable in class sbrt.shell.mng.fba.ObjectiveFunctionManager
The keyword used to denote the file containing objective functions.
OBJ_FUNCT_FILE_FORMAT - Static variable in class sbrt.shell.mng.fba.ObjectiveFunctionManager
The keyword used to denote the format of the file containing objective functions.
OBJ_VALUE - Static variable in class sbrt.shell.text.fba.FbaOptHeaderFormatterV1
The header used to indicate the value of the objective function.
OBJ_VALUE - Static variable in class sbrt.shell.text.fba.FbaOptHeaderParserV1
The header used to indicate the value of the objective function.
objectIterator() - Method in class sbrt.shell.io.SerializedInputFile
Returns an object iterator over this file.
OBJECTIVE_FUNCTION - Static variable in class sbrt.shell.mng.fba.FbaOptManager
The keyword used to denote an objective function.
ObjectiveFunctionManager - Class in sbrt.shell.mng.fba
This class is used to manage objective function processes.
ObjectiveFunctionManager() - Constructor for class sbrt.shell.mng.fba.ObjectiveFunctionManager
 
ObjFunAnalysis<F extends Fluxome> - Class in sbrt.kernel.fba.proc
This class is used to perform objective function analyses.
ObjFunAnalysis(FbaOptimizer<F>) - Constructor for class sbrt.kernel.fba.proc.ObjFunAnalysis
Constructs a new objective function process.
OFF - Static variable in class sbrt.kernel.fba.IrrevRxnFluxomeV1
The constraint used by default for all source reactions: [0, 0].
OFF - Static variable in class sbrt.kernel.fba.MixedFluxomeV1
The constraint used by default for source reactions and reversible exchange reactions: [0, 0].
ON - Static variable in class sbrt.kernel.fba.IrrevRxnFluxomeV1
The constraint used by default for all internal and sink reactions: [0, Infinity).
oppositeSign(double, double) - Static method in class sbrt.kernel.utilities.Util
Indicates if the provided numbers are of opposite sign.
oppositeSign(int, int) - Static method in class sbrt.kernel.utilities.Util
Indicates if the provided numbers are of opposite sign.
OPTIMIZATION_SENSE - Static variable in class sbrt.shell.mng.fba.FbaOptManager
The keyword used to denote the optimization sense, or direction.
optimize() - Method in class sbrt.ext.cplex.CplexSolver
Computes the optimal value of the current objective function in the direction of the current optimization sense.
optimize() - Method in class sbrt.ext.glpk.GlpkSolver
Computes the optimal value of the current objective function in the current optimization sense.
optimize() - Method in interface sbrt.kernel.math.optimization.ProgramSolver
Computes the optimal value of the current objective function in the direction of the current optimization sense.
optionalKeywords - Static variable in class plug_in_example.shell.GreetingManager
The set of optional keywords in the ManagerInput objects supplied to instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.AbstractProcessManager
The set of optional keywords in the ManagerInput objects supplied to instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.algebra.LinearCombConverterManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.algebra.LinearSolverManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.algebra.MatrixConverterManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.algebra.MultipleVectorsConverterManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.algebra.SingleVectorConverterManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.comb.SingleElementUnionManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.comb.StrictSingleElementUnionManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.BiggSbmlReaderManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.CatalystDeletionManager
The set of optional keywords in the ManagerInput objects supplied to instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.CdHarFluxVectorManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.CvCatalystDeletionManager
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.CvFbaOptManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.CvMsFluxIntervalManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.CvObjectiveFunctionManager
The set of optional keywords in the ManagerInput objects supplied to instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.CvRevRxnFluxIntervalManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.CvRxnDeletionManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.CvSimpleFluxIntervalManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.ExtremeCurrentManager
The set of optional keywords in the ManagerInput objects supplied to instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.FbaManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.FbaOptManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.FbaSolverManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.FluxActivityManager
The set of optional keywords in the ManagerInput objects supplied to instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.FluxCapManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.FluxPlasticityManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.InitialPointManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.MetatoolInputReaderManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.MetatoolInputWriterManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.MetatoolOutputReaderManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.MsFluxIntervalManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.MsFluxomeReducerManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.NetworkInfoManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.ObjectiveFunctionManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.PalssonSbmlReaderManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.RandomConstraintsManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.RandomObjectiveManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.RedundRxnRemoverManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.ReverseRxnFluxIntervalManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.RevRxnBreakerManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.RxnDeletionManager
The set of optional keywords in the ManagerInput objects supplied to instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.SimpleFluxIntervalManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.SimpleRxnFileTransManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.SlpCycleIdManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.fba.WwFluxomeReducerManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.geom.CdHarManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.graph_theory.CycleIdManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.graph_theory.GraphInfoManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.graph_theory.PathIdManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.graph_theory.UniqueCycleIdManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.stat.CorrelationManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.stat.KendallTauManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.stat.MannWhitneyUManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.utilities.IntervalComparisonManager
The set of keywords understood, but not required, by this process manager.
optionalKeywords - Static variable in class sbrt.shell.mng.utilities.VariableParticipationManager
The set of keywords understood, but not required, by instances of this class.
optionalKeywords - Static variable in class sbrt.shell.mng.utilities.VectorComparisonManager
The set of keywords understood, but not required, by this process manager.
OptSense - Enum in sbrt.kernel.math.optimization
This enum type is used to represent the sense, or direction, of an optimization problem.
Or<C> - Class in sbrt.kernel.utilities
This class is used to represent the logical relationship "or".
Or(Collection<C>) - Constructor for class sbrt.kernel.utilities.Or
Constructs a new "or" relationship.
OUTPUT_FILE_FORMAT - Static variable in class sbrt.shell.mng.AbstractProcessManager
The keyword used to denote the name of an output file format.
OUTPUT_FILE_NAME - Static variable in class sbrt.shell.mng.AbstractProcessManager
The keyword used to denote the name of the output file.
OUTPUT_FILE_NAME_FILE - Static variable in class sbrt.shell.mng.AbstractProcessManager
The keyword used to denote the name of a file containing a list of file names for other output files.
OutputFile<T> - Interface in sbrt.shell.io
This interface is used to represent output files.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z