| Package | Description |
|---|---|
| de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels |
Provides
DifferentiableStatisticalModels that are directed graphical models. |
| de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif |
| Constructor and Description |
|---|
MarkovModelDiffSM(AlphabetContainer alphabet,
int length,
double ess,
boolean plugInParameters,
InhomogeneousMarkov structureMeasure,
DurationDiffSM lengthPenalty)
This constructor creates an instance with an prior for the modeled length.
|
MarkovModelDiffSM(AlphabetContainer alphabet,
int length,
double ess,
boolean plugInParameters,
int order,
DurationDiffSM lengthPenalty)
This constructor creates an instance with an prior for the modeled length.
|
| Modifier and Type | Class and Description |
|---|---|
class |
MixtureDurationDiffSM
This class implements a mixture of
DurationDiffSMs. |
class |
SkewNormalLikeDurationDiffSM
This class implements a skew normal like discrete truncated distribution.
|
class |
UniformDurationDiffSM
This scoring function implements a uniform distribution for positions.
|
| Constructor and Description |
|---|
ExtendedZOOPSDiffSM(boolean type,
int length,
int starts,
boolean plugIn,
HomogeneousDiffSM bg,
DifferentiableStatisticalModel[] motif,
DurationDiffSM[] posPrior,
boolean plugInBg)
This constructor creates an instance of
ExtendedZOOPSDiffSM that allows to have one site of the specified motifs in a Sequence. |
ExtendedZOOPSDiffSM(boolean type,
int length,
int starts,
boolean plugIn,
HomogeneousDiffSM bg,
DifferentiableStatisticalModel motif,
DurationDiffSM posPrior,
boolean plugInBg)
This constructor creates an instance of
ExtendedZOOPSDiffSM that is either an OOPS or a ZOOPS model depending on the chosen type. |
MixtureDurationDiffSM(int starts,
DurationDiffSM... function)
The main constructor of a
MixtureDurationDiffSM. |