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## Uses of Interface
de.jstacs.motifDiscovery.history.History

Packages that use History
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.motifDiscovery.history |

Uses of History in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that return History
`static History[][]` | `MutableMotifDiscovererToolbox.createHistoryArray(ScoringFunction[] funs, History template)` This method creates a History-array that can be used in an optimization.

Methods in de.jstacs.motifDiscovery with parameters of type History
`static void` | `MutableMotifDiscovererToolbox.clearHistoryArray(History[][] history)` This method clears all elements of an History-array, so that it can be used again.
`static History[][]` | `MutableMotifDiscovererToolbox.createHistoryArray(ScoringFunction[] funs, History template)` This method creates a History-array that can be used in an optimization.
`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 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 History in de.jstacs.motifDiscovery.history

Classes in de.jstacs.motifDiscovery.history that implement History
`class` | `CappedHistory` This class combines a threshold on the number of steps which can be performed with any other `History`.
`class` | `NoRevertHistory` This class implements a history that allows operations, that are not a priorily forbidden and do not create a configuration that has already be considered.
`class` | `RestrictedRepeatHistory` This class implements a history that allows operations (i.e. a pair of `int`), that are not a priorily forbidden and that are done before less than a specified threshold.
`class` | `SimpleHistory` This class implements a simple history that has a limited memory that will be used cyclicly.

Methods in de.jstacs.motifDiscovery.history that return History
`History` | `History.clone()` This method returns a deep copy of the instance

Constructors in de.jstacs.motifDiscovery.history with parameters of type History
`CappedHistory(int t, History h)` This constructor creates an instance that allows at most `t` steps using the history `h`.

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