See: Description
| Interface | Description |
|---|---|
| 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 | Description |
|---|---|
| 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 | Description |
|---|---|
| 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 |