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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) - Constructor for class de.jstacs.algorithms.optimization.OneDimensionalSubFunction

Creates a new OneDimensionalSubFunction from a Function f for the line search.

OneMinusPearsonCorrelationCoefficient() - Constructor for class de.jstacs.utils.PFMComparator.OneMinusPearsonCorrelationCoefficient

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.

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.

order(double[], boolean) - Static method in class de.jstacs.utils.ToolBox

This method computes the order of the elements to obtain a sorted array.

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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