Package | Description |
---|---|
de.jstacs.motifDiscovery |
This package provides the framework including the interface for any de novo motif discoverer.
|
de.jstacs.parameters |
This package provides classes for parameters that establish a general convention for the description of parameters
as defined in the
Parameter -interface. |
de.jstacs.utils |
This package contains a bundle of useful classes and interfaces like ...
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Modifier and Type | Method and Description |
---|---|
static ComparableElement<double[],Double>[] |
MutableMotifDiscovererToolbox.getSortedInitialParameters(DifferentiableSequenceScore[] funs,
MutableMotifDiscovererToolbox.InitMethodForDiffSM[] init,
DiffSSBasedOptimizableFunction opt,
int n,
OutputStream stream,
int optimizationSteps)
This method allows to initialize the
DifferentiableSequenceScore using different MutableMotifDiscovererToolbox.InitMethodForDiffSM . |
Modifier and Type | Method and Description |
---|---|
int |
ParameterSetTagger.RankEntryComparator.compare(Map.Entry<K,ComparableElement<V,Integer>> o1,
Map.Entry<K,ComparableElement<V,Integer>> o2) |
int |
ParameterSetTagger.RankEntryComparator.compare(Map.Entry<K,ComparableElement<V,Integer>> o1,
Map.Entry<K,ComparableElement<V,Integer>> o2) |
String |
ParameterSetTagger.toString(Comparator<Map.Entry<String,ComparableElement<Parameter,Integer>>> ec)
This method allows to get a String representation where the tagged parameters are sorted in some specific way.
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Modifier and Type | Method and Description |
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static ComparableElement<String,Double>[] |
PFMComparator.find(ComplementableDiscreteAlphabet abc,
double[][] pfm,
ArrayList<AbstractMap.SimpleEntry<String,double[][]>> knownPFMs,
PFMComparator.PFMDistance distance,
int minOverlap,
int allowMiniShift,
boolean pValues,
double threshold)
This methods finds for a user specified PFM
pfm similar PFMs in a list of known PFMs. |
Modifier and Type | Method and Description |
---|---|
int |
ComparableElement.compareTo(ComparableElement<E,C> o) |