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

Packages that use SafeOutputStream
de.jstacs.algorithms.optimization | Provides classes for different types of algorithms that are not directly linked to the modelling components of Jstacs: Algorithms on graphs, algorithms for numerical optimization, and a basic alignment algorithm.
de.jstacs.classifier.scoringFunctionBased | Provides the classes for `Classifier`s that are based on `ScoringFunction`s.
de.jstacs.models.discrete.inhomogeneous | This package contains various inhomogeneous models.
de.jstacs.models.mixture | This package is the super package for any mixture model.
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer

Uses of SafeOutputStream in de.jstacs.algorithms.optimization

Methods in de.jstacs.algorithms.optimization with parameters of type SafeOutputStream
`static int` | `Optimizer.conjugateGradientsFR(DifferentiableFunction f, double[] currentValues, Optimizer.TerminationCondition terminationMode, double eps, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, Time t)` The conjugate gradient algorithm by Fletcher and Reeves.
`static int` | `Optimizer.conjugateGradientsPR(DifferentiableFunction f, double[] currentValues, Optimizer.TerminationCondition terminationMode, double eps, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, Time t)` The conjugate gradient algorithm by Polak and Ribière.
`static int` | `Optimizer.conjugateGradientsPRP(DifferentiableFunction f, double[] currentValues, Optimizer.TerminationCondition terminationMode, double eps, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, Time t)` The conjugate gradient algorithm by Polak and Ribière called "Polak-Ribière-Positive".
`static int` | `Optimizer.limitedMemoryBFGS(DifferentiableFunction f, double[] currentValues, byte m, Optimizer.TerminationCondition terminationMode, double eps, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, Time t)` The Broyden-Fletcher-Goldfarb-Shanno version of limited memory quasi-Newton methods.
`static int` | `Optimizer.optimize(byte algorithm, DifferentiableFunction f, double[] currentValues, Optimizer.TerminationCondition terminationMode, double eps, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out)` This method enables you to use all different implemented optimization algorithms by only one method.
`static int` | `Optimizer.optimize(byte algorithm, DifferentiableFunction f, double[] currentValues, Optimizer.TerminationCondition terminationMode, double eps, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, Time t)` This method enables you to use all different implemented optimization algorithms by only one method.
`static int` | `Optimizer.quasiNewtonBFGS(DifferentiableFunction f, double[] currentValues, Optimizer.TerminationCondition terminationMode, double eps, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, Time t)` The Broyden-Fletcher-Goldfarb-Shanno version of the quasi-Newton method.
`static int` | `Optimizer.quasiNewtonDFP(DifferentiableFunction f, double[] currentValues, Optimizer.TerminationCondition terminationMode, double eps, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, Time t)` The Davidon-Fletcher-Powell version of the quasi-Newton method.
`static int` | `Optimizer.steepestDescent(DifferentiableFunction f, double[] currentValues, Optimizer.TerminationCondition terminationMode, double eps, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, Time t)` The steepest descent.

Uses of SafeOutputStream in de.jstacs.classifier.scoringFunctionBased

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

Uses of SafeOutputStream in de.jstacs.models.discrete.inhomogeneous

Fields in de.jstacs.models.discrete.inhomogeneous declared as SafeOutputStream
`protected SafeOutputStream` | `InhomogeneousDGM.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.models.mixture

Fields in de.jstacs.models.mixture declared as SafeOutputStream
`protected SafeOutputStream` | `AbstractMixtureModel.sostream` This is the stream for writing information while training.

Uses of SafeOutputStream in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery with parameters of type SafeOutputStream
`static boolean` | `MutableMotifDiscovererToolbox.doHeuristicSteps(ScoringFunction[] funs, Sample[] data, double[][] weights, OptimizableFunction opt, SafeOutputStream out, boolean breakOnChanged, History[][] hist, int[][] minimalNewLength)` This method tries to make some heuristic step if at least one `MutableMotifDiscovererToolbox.InitMethodForScoringFunction` is a `MutableMotifDiscoverer`.
`static ComparableElement<double[],Double>[]` | `MutableMotifDiscovererToolbox.getSortedInitialParameters(Sample[] data, ScoringFunction[] funs, MutableMotifDiscovererToolbox.InitMethodForScoringFunction[] init, OptimizableFunction opt, int n, SafeOutputStream stream)` This method allows to initialize the `MutableMotifDiscovererToolbox.InitMethodForScoringFunction` using different `MutableMotifDiscovererToolbox.InitMethodForScoringFunction`.
`static double[][]` | `MutableMotifDiscovererToolbox.optimize(ScoringFunction[] funs, OptimizableFunction opt, byte algorithm, double eps, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, boolean breakOnChanged, History[][] hist, int[][] minimalNewLength, OptimizableFunction.KindOfParameter plugIn)` This method tries to optimize the problem at hand as good as possible.
`static double[][]` | `MutableMotifDiscovererToolbox.optimize(ScoringFunction[] funs, OptimizableFunction opt, byte algorithm, double eps, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, boolean breakOnChanged, History template, OptimizableFunction.KindOfParameter plugIn)` This method tries to optimize the problem at hand as good as possible.

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