Uses of Class
de.jstacs.utils.SafeOutputStream

Packages that use SafeOutputStream

Package	Description
de.jstacs.classifiers.differentiableSequenceScoreBased	Provides the classes for Classifiers that are based on SequenceScores. It includes a sub-package for discriminative objective functions, namely conditional likelihood and supervised posterior, and a separate sub-package for the parameter priors, that can be used for the supervised posterior.
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

Modifier and Type	Field and Description
protected SafeOutputStream	ScoreClassifier.sostream This stream is used for comments, e.g.

Uses of SafeOutputStream in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery with parameters of type SafeOutputStream

Modifier and Type	Method and Description
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.
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

Modifier and Type	Field and Description
protected SafeOutputStream	InhomogeneousDGTrainSM.sostream This stream is used for comments, computation steps/results or any other kind of output during the training, ...

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous with parameters of type SafeOutputStream

Modifier and Type	Method and Description
void	MEM.train(SequenceIterator s, byte algo, TerminationCondition condition, SafeOutputStream sostream) This method approximates the distribution either analytically or numerically.

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

Fields in de.jstacs.sequenceScores.statisticalModels.trainable.hmm declared as SafeOutputStream

Modifier and Type	Field and Description
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

Modifier and Type	Field and Description
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

Modifier and Type	Method and Description
static SafeOutputStream	SafeOutputStream.getSafeOutputStream(OutputStream out) This method returns an instance of SafeOutputStream for a given OutputStream.