Uses of Class
de.jstacs.utils.SafeOutputStream

Packages that use SafeOutputStream
de.jstacs.classifier.scoringFunctionBased Provides the classes for Classifiers that are based on ScoringFunctions. 
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 
de.jstacs.utils This package contains a bundle of useful classes and interfaces like ... 
 

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, SFBasedOptimizableFunction 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 MutableMotifDiscovererToolbox.InitMethodForScoringFunction is a MutableMotifDiscoverer.
static boolean MutableMotifDiscovererToolbox.findModification(int clazz, int motif, MutableMotifDiscoverer mmd, ScoringFunction[] score, Sample[] data, SFBasedOptimizableFunction 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 ComparableElement<double[],Double>[] MutableMotifDiscovererToolbox.getSortedInitialParameters(ScoringFunction[] funs, MutableMotifDiscovererToolbox.InitMethodForScoringFunction[] init, SFBasedOptimizableFunction opt, int n, SafeOutputStream stream, int optimizationSteps)
          This method allows to initialize the MutableMotifDiscovererToolbox.InitMethodForScoringFunction using different MutableMotifDiscovererToolbox.InitMethodForScoringFunction.
static double[][] MutableMotifDiscovererToolbox.optimize(ScoringFunction[] funs, SFBasedOptimizableFunction opt, byte algorithm, double eps, 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(ScoringFunction[] funs, SFBasedOptimizableFunction opt, byte algorithm, double eps, 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.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.