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## Uses of Class
de.jstacs.utils.SafeOutputStream

Packages that use SafeOutputStream
de.jstacs.classifiers.differentiableSequenceScoreBased | Provides the classes for `Classifier`s that are based on `SequenceScore`s.
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous | This package contains various inhomogeneous models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm | The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.sequenceScores.statisticalModels.trainable.mixture | This package is the super package for any mixture model.
de.jstacs.utils | This package contains a bundle of useful classes and interfaces like ...

Uses of SafeOutputStream in de.jstacs.classifiers.differentiableSequenceScoreBased

Fields in de.jstacs.classifiers.differentiableSequenceScoreBased declared as SafeOutputStream
`protected SafeOutputStream` | `ScoreClassifier.sostream` This stream is used for comments, e.g. during the training, ... .

Uses of SafeOutputStream in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery with parameters of type SafeOutputStream
`static boolean` | `MutableMotifDiscovererToolbox.doHeuristicSteps(DifferentiableSequenceScore[] funs, DataSet[] data, double[][] weights, DiffSSBasedOptimizableFunction opt, DifferentiableFunction neg, byte algorithm, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, boolean breakOnChanged, History[][] hist, int[][] minimalNewLength, boolean maxPos)` This method tries to make some heuristic step if at least one `DifferentiableSequenceScore` is a `MutableMotifDiscoverer`.
`static boolean` | `MutableMotifDiscovererToolbox.findModification(int clazz, int motif, MutableMotifDiscoverer mmd, DifferentiableSequenceScore[] score, DataSet[] data, double[][] weights, DiffSSBasedOptimizableFunction opt, DifferentiableFunction neg, byte algo, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, History hist, int minimalNewLength, boolean maxPos)` This method tries to find a modification, i.e. shifting, shrinking, or expanding a motif, that is promising.
`static double[][]` | `MutableMotifDiscovererToolbox.optimize(DifferentiableSequenceScore[] funs, DiffSSBasedOptimizableFunction opt, byte algorithm, AbstractTerminationCondition condition, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, boolean breakOnChanged, History[][] hist, int[][] minimalNewLength, OptimizableFunction.KindOfParameter plugIn, boolean maxPos)` This method tries to optimize the problem at hand as good as possible.
`static double[][]` | `MutableMotifDiscovererToolbox.optimize(DifferentiableSequenceScore[] funs, DiffSSBasedOptimizableFunction opt, byte algorithm, AbstractTerminationCondition condition, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, boolean breakOnChanged, History template, OptimizableFunction.KindOfParameter plugIn, boolean maxPos)` This method tries to optimize the problem at hand as good as possible.

Uses of SafeOutputStream in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous

Fields in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous declared as SafeOutputStream
`protected SafeOutputStream` | `InhomogeneousDGTrainSM.sostream` This stream is used for comments, computation steps/results or any other kind of output during the training, ... etc.

Uses of SafeOutputStream in de.jstacs.sequenceScores.statisticalModels.trainable.hmm

Fields in de.jstacs.sequenceScores.statisticalModels.trainable.hmm declared as SafeOutputStream
`protected SafeOutputStream` | `AbstractHMM.sostream` This is the stream for writing information while training.

Uses of SafeOutputStream in de.jstacs.sequenceScores.statisticalModels.trainable.mixture

Fields in de.jstacs.sequenceScores.statisticalModels.trainable.mixture declared as SafeOutputStream
`protected SafeOutputStream` | `AbstractMixtureTrainSM.sostream` This is the stream for writing information while training.

Uses of SafeOutputStream in de.jstacs.utils

Methods in de.jstacs.utils that return SafeOutputStream
`static SafeOutputStream` | `SafeOutputStream.getSafeOutputStream(OutputStream out)` This method returns an instance of `SafeOutputStream` for a given `OutputStream`.

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