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 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 
 

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.