| Package | Description |
|---|---|
| de.jstacs.classifiers.differentiableSequenceScoreBased |
Provides the classes for
Classifiers that are based on SequenceScores.It includes a sub-package for discriminative objective functions, namely conditional likelihood and supervised posterior, and a separate sub-package for the parameter priors, that can be used for the supervised posterior. |
| de.jstacs.motifDiscovery |
This package provides the framework including the interface for any de novo motif discoverer.
|
| de.jstacs.motifDiscovery.history |
| Modifier and Type | Field and Description |
|---|---|
protected History |
ScoreClassifier.template
The default history
|
| Modifier and Type | Method and Description |
|---|---|
static History[][] |
MutableMotifDiscovererToolbox.createHistoryArray(DifferentiableSequenceScore[] funs,
History template)
This method creates a History-array that can be used in an optimization.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
MutableMotifDiscovererToolbox.clearHistoryArray(History[][] history)
This method clears all elements of an History-array, so that it can be used again.
|
static History[][] |
MutableMotifDiscovererToolbox.createHistoryArray(DifferentiableSequenceScore[] funs,
History template)
This method creates a History-array that can be used in an optimization.
|
static boolean |
MutableMotifDiscovererToolbox.doHeuristicSteps(DifferentiableSequenceScore[] funs,
DataSet[] data,
double[][] weights,
DiffSSBasedOptimizableFunction opt,
DifferentiableFunction neg,
byte algorithm,
double linEps,
StartDistanceForecaster startDistance,
SafeOutputStream out,
boolean breakOnChanged,
History[][] hist,
int[][] minimalNewLength,
boolean maxPos)
This method tries to make some heuristic step if at least one
DifferentiableSequenceScore is a MutableMotifDiscoverer. |
static boolean |
MutableMotifDiscovererToolbox.findModification(int clazz,
int motif,
MutableMotifDiscoverer mmd,
DifferentiableSequenceScore[] score,
DataSet[] data,
double[][] weights,
DiffSSBasedOptimizableFunction opt,
DifferentiableFunction neg,
byte algo,
double linEps,
StartDistanceForecaster startDistance,
SafeOutputStream out,
History hist,
int minimalNewLength,
boolean maxPos)
This method tries to find a modification, i.e.
|
static double[][] |
MutableMotifDiscovererToolbox.optimize(DifferentiableSequenceScore[] funs,
DiffSSBasedOptimizableFunction opt,
byte algorithm,
AbstractTerminationCondition condition,
double linEps,
StartDistanceForecaster startDistance,
SafeOutputStream out,
boolean breakOnChanged,
History[][] hist,
int[][] minimalNewLength,
OptimizableFunction.KindOfParameter plugIn,
boolean maxPos)
This method tries to optimize the problem at hand as good as possible.
|
static double[][] |
MutableMotifDiscovererToolbox.optimize(DifferentiableSequenceScore[] funs,
DiffSSBasedOptimizableFunction opt,
byte algorithm,
AbstractTerminationCondition condition,
double linEps,
StartDistanceForecaster startDistance,
SafeOutputStream out,
boolean breakOnChanged,
History template,
OptimizableFunction.KindOfParameter plugIn,
boolean maxPos)
This method tries to optimize the problem at hand as good as possible.
|
| Modifier and Type | Class and Description |
|---|---|
class |
CappedHistory
This class combines a threshold on the number of steps which can be performed with any other
History. |
class |
NoRevertHistory
This class implements a history that allows operations, that are not a
priorily forbidden and do not create a configuration that has already be
considered.
|
class |
RestrictedRepeatHistory
This class implements a history that allows operations (i.e.
|
class |
SimpleHistory
This class implements a simple history that has a limited memory that will be
used cyclicly.
|
| Modifier and Type | Method and Description |
|---|---|
History |
History.clone()
This method returns a deep copy of the instance
|
| Constructor and Description |
|---|
CappedHistory(int t,
History h)
This constructor creates an instance that allows at most
t steps using the history h. |