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

Packages that use History

de.jstacs.classifiers.differentiableSequenceScoreBased	Provides the classes for Classifiers that are based on SequenceScores.
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.classifiers.differentiableSequenceScoreBased

Fields in de.jstacs.classifiers.differentiableSequenceScoreBased declared as History

protected History

ScoreClassifier.template The default history

Uses of History in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that return History

static History[][]

MutableMotifDiscovererToolbox.createHistoryArray(DifferentiableSequenceScore[] 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(DifferentiableSequenceScore[] funs, History template) This method creates a History-array that can be used in an optimization.
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. shifting, shrinking, or expanding a motif, that is promising.
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 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.