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Description
Interface Summary | |
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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 | |
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KMereStatistic | This class enables the user to get some statistics of a DataSet 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 | |
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MotifDiscoverer.KindOfProfile | This enum can be used to determine which kind of profile
should be returned. |
MutableMotifDiscovererToolbox.InitMethodForDiffSM | This enum defines some constants for the method MutableMotifDiscovererToolbox.getSortedInitialParameters(DifferentiableSequenceScore[], InitMethodForDiffSM[], DiffSSBasedOptimizableFunction, int, OutputStream, int) . |
SignificantMotifOccurrencesFinder.RandomSeqType |
This package provides the framework including the interface for any de novo motif discoverer.
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