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Packages that use SafeOutputStream | |
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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 |
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Methods in de.jstacs.algorithms.optimization with parameters of type SafeOutputStream | |
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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 |
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Fields in de.jstacs.classifier.scoringFunctionBased declared as SafeOutputStream | |
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protected SafeOutputStream |
ScoreClassifier.sostream
This stream is used for comments, e.g. during the training, ... . |
Uses of SafeOutputStream in de.jstacs.models.discrete.inhomogeneous |
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Fields in de.jstacs.models.discrete.inhomogeneous declared as SafeOutputStream | |
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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 |
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Fields in de.jstacs.models.mixture declared as SafeOutputStream | |
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protected SafeOutputStream |
AbstractMixtureModel.sostream
This is the stream for writing information while training. |
Uses of SafeOutputStream in de.jstacs.motifDiscovery |
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Methods in de.jstacs.motifDiscovery with parameters of type SafeOutputStream | |
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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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