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## O

offset - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.InhConstraint
  This array is used to find the start indices of the conditional distributions.
offset - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission
  The offset of the parameter indexes
offset - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.TransitionElement
  The internally used parameter offset.
OneDataSetLogGenDisMixFunction - Class in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix
  This class implements the the following function
  where is the weight for sequence and class .
OneDataSetLogGenDisMixFunction(int, DifferentiableSequenceScore[], DataSet, double[][], LogPrior, double[], boolean, boolean) - Constructor for class de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.OneDataSetLogGenDisMixFunction
  The constructor for creating an instance that can be used in an `Optimizer`.
OneDimensionalFunction - Class in de.jstacs.algorithms.optimization
  This class implements the interface `Function` for an one-dimensional function.
OneDimensionalFunction() - Constructor for class de.jstacs.algorithms.optimization.OneDimensionalFunction
OneDimensionalSubFunction - Class in de.jstacs.algorithms.optimization
  This class is used to do the line search.
OneDimensionalSubFunction(Function, double[], double[]) - Constructor for class de.jstacs.algorithms.optimization.OneDimensionalSubFunction
  Creates a new `OneDimensionalSubFunction` from a `Function` `f` for the line search.
openRConnection(String, String, String) - Static method in class de.jstacs.utils.RUtils
  This method opens an `RConnection`.
operationAllowed(int...) - Method in class de.jstacs.motifDiscovery.history.CappedHistory
operationAllowed(int...) - Method in interface de.jstacs.motifDiscovery.history.History
  Returns `true` if the specified operation is allowed, i.e. it does not conflict with any operation from the history.
operationAllowed(int...) - Method in class de.jstacs.motifDiscovery.history.NoRevertHistory
operationAllowed(int...) - Method in class de.jstacs.motifDiscovery.history.RestrictedRepeatHistory
operationAllowed(int...) - Method in class de.jstacs.motifDiscovery.history.SimpleHistory
operationPerfomed(int...) - Method in class de.jstacs.motifDiscovery.history.CappedHistory
operationPerfomed(int...) - Method in interface de.jstacs.motifDiscovery.history.History
  This method puts an operation to the history.
operationPerfomed(int...) - Method in class de.jstacs.motifDiscovery.history.NoRevertHistory
operationPerfomed(int...) - Method in class de.jstacs.motifDiscovery.history.RestrictedRepeatHistory
operationPerfomed(int...) - Method in class de.jstacs.motifDiscovery.history.SimpleHistory
OptimizableFunction - Class in de.jstacs.classifiers.differentiableSequenceScoreBased
  This is the main function for the `ScoreClassifier`.
OptimizableFunction() - Constructor for class de.jstacs.classifiers.differentiableSequenceScoreBased.OptimizableFunction
OptimizableFunction.KindOfParameter - Enum in de.jstacs.classifiers.differentiableSequenceScoreBased
  This `enum` defines the kinds of parameters that can be returned by the method `OptimizableFunction.getParameters(KindOfParameter)`.
optimize(byte, DifferentiableFunction, double[], TerminationCondition, double, StartDistanceForecaster, OutputStream) - Static method in class de.jstacs.algorithms.optimization.Optimizer
  This method enables you to use all different implemented optimization algorithms by only one method.
optimize(byte, DifferentiableFunction, double[], TerminationCondition, double, StartDistanceForecaster, OutputStream, Time) - Static method in class de.jstacs.algorithms.optimization.Optimizer
  This method enables you to use all different implemented optimization algorithms by only one method.
optimize(DifferentiableSequenceScore[], DiffSSBasedOptimizableFunction, byte, AbstractTerminationCondition, double, StartDistanceForecaster, SafeOutputStream, boolean, History, OptimizableFunction.KindOfParameter, boolean) - Static method in class de.jstacs.motifDiscovery.MutableMotifDiscovererToolbox
  This method tries to optimize the problem at hand as good as possible.
optimize(DifferentiableSequenceScore[], DiffSSBasedOptimizableFunction, byte, AbstractTerminationCondition, double, StartDistanceForecaster, SafeOutputStream, boolean, History[][], int[][], OptimizableFunction.KindOfParameter, boolean) - Static method in class de.jstacs.motifDiscovery.MutableMotifDiscovererToolbox
  This method tries to optimize the problem at hand as good as possible.
optimizeHidden - Variable in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.AbstractMixtureDiffSM
  This `boolean` indicates whether to optimize the hidden variables of this instance.
optimizeModel - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM
  A switch for each model whether to optimize/adjust or not.
Optimizer - Class in de.jstacs.algorithms.optimization
  This class can be used for optimization purposes.
Optimizer() - Constructor for class de.jstacs.algorithms.optimization.Optimizer
order - Variable in class de.jstacs.algorithms.graphs.tensor.Tensor
  The order of the tensor.
order - Variable in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BayesianNetworkDiffSM
  The network structure, used internally.
order - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.HomogeneousTrainSM
  The order of the model.
original - Variable in class de.jstacs.data.sequences.MappedDiscreteSequence
  The original `Sequence`.
originalAlphabetContainer - Variable in class de.jstacs.data.sequences.MappedDiscreteSequence
  The original `AlphabetContainer`.
overlaps(LocatedSequenceAnnotationWithLength) - Method in class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength
  Returns `true` if this `LocatedSequenceAnnotationWithLength` overlaps with the location of `second`.

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