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## Package de.jstacs.motifDiscovery

This package provides the framework including the interface for any de novo motif discoverer

See:
Description

Interface Summary
MotifDiscoverer | This is the interface that any tool for de-novo motif discovery should implement.
Mutable | This interface allows to modify a motif model.
MutableMotifDiscoverer | This is the interface that any tool for de-novo motif discovery should implement that allows any modify-operations like shift, shrink and expand.
SignificantMotifOccurrencesFinder.JoinMethod | Interface for methods that combine several profiles over the same sequence into one common profile

Class Summary
KMereStatistic | This class enables the user to get some statistics of a `Sample` in an easy way.
MotifDiscovererToolBox | This class contains static methods for the `MotifDiscoverer`.
MotifDiscoveryAssessment | This class enables the user to assess the prediction of motif occurrences
MutableMotifDiscovererToolbox | This class contains some important methods for the initiation and optimization of `MutableMotifDiscoverer`.
SignificantMotifOccurrencesFinder | This class enables the user to predict motif occurrences given a specific significance level.
SignificantMotifOccurrencesFinder.SumOfProbabilities | Joins several profiles containing log-probabilities into one profile containing the logarithm of the sum of the probabilities of the single profiles.

Enum Summary
MotifDiscoverer.KindOfProfile | This `enum` can be used to determine which kind of profile should be returned.
MutableMotifDiscovererToolbox.InitMethodForScoringFunction | This enum defines some constants for the method `MutableMotifDiscovererToolbox.getSortedInitialParameters(ScoringFunction[], InitMethodForScoringFunction[], SFBasedOptimizableFunction, int, OutputStream, int)`.
SignificantMotifOccurrencesFinder.RandomSeqType |

## Package de.jstacs.motifDiscovery Description

This package provides the framework including the interface for any de novo motif discoverer.

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