| Package | Description |
|---|---|
| de.jstacs.motifDiscovery |
This package provides the framework including the interface for any de novo motif discoverer.
|
| de.jstacs.sequenceScores.statisticalModels.differentiable |
Provides all
DifferentiableStatisticalModels, which can compute the gradient with
respect to their parameters for a given input Sequence. |
| de.jstacs.sequenceScores.statisticalModels.differentiable.mixture |
Provides
DifferentiableSequenceScores that are mixtures of other DifferentiableSequenceScores. |
| de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif | |
| de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif |
| Modifier and Type | Method and Description |
|---|---|
static MotifDiscoverer.KindOfProfile |
MotifDiscoverer.KindOfProfile.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static MotifDiscoverer.KindOfProfile[] |
MotifDiscoverer.KindOfProfile.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
| Modifier and Type | Method and Description |
|---|---|
double[] |
MotifDiscoverer.getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile kind)
Returns the profile of the scores for component
component
and motif motif at all possible start positions of the motif
in the sequence sequence beginning at startpos. |
static ImageResult |
MotifDiscovererToolBox.plot(MotifDiscoverer motifDisc,
int component,
int motif,
Sequence sequence,
int startpos,
REnvironment r,
int width,
int height,
MotifDiscoverer.KindOfProfile kind)
This method creates a simple plot of the profile of scores for a sequence
and a start position.
|
static ImageResult |
MotifDiscovererToolBox.plotAndAnnotate(MotifDiscoverer motifDisc,
int component,
int motif,
Sequence sequence,
int startpos,
REnvironment r,
int width,
int height,
double yMin,
double yMax,
double threshold,
MotifDiscoverer.KindOfProfile kind)
This method creates a plot of the profile of scores for a sequence and a
start position and annotates bindings sites in the plot that have a higher
score than
threshold. |
| Modifier and Type | Method and Description |
|---|---|
double[] |
MappingDiffSM.getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile kind) |
double[] |
IndependentProductDiffSM.getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile dist) |
| Modifier and Type | Method and Description |
|---|---|
double[] |
MixtureDiffSM.getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile kind) |
| Modifier and Type | Method and Description |
|---|---|
double[] |
ExtendedZOOPSDiffSM.getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile dist) |
| Modifier and Type | Method and Description |
|---|---|
double[] |
ZOOPSTrainSM.getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile kind) |