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, 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 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.
 

Uses of History in de.jstacs.motifDiscovery.history
 

Classes in de.jstacs.motifDiscovery.history that implement History
 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.
 

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