Uses of Interface
de.jstacs.data.RecyclableSequenceEnumerator

Packages that use RecyclableSequenceEnumerator

Package	Description
de.jstacs.data	Provides classes for the representation of data. The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets, Sequence and its sub-classes to represent continuous and discrete sequences, and DataSet to represent data sets comprising a set of sequences.
de.jstacs.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer.

Uses of RecyclableSequenceEnumerator in de.jstacs.data

Classes in de.jstacs.data that implement RecyclableSequenceEnumerator

Modifier and Type	Class and Description
static class	DataSet.ElementEnumerator This class can be used to have a fast sequential access to a DataSet.
class	DataSetKMerEnumerator Class for an RecyclableSequenceEnumerator of Sequences that enumerates all k-mers that exist in a given DataSet, optionally ignoring reverse complements.
class	DiscreteSequenceEnumerator This class enumerates over all Sequences of a specific AlphabetContainer and length.
class	SequenceEnumeration This class implements a RecyclableSequenceEnumerator on user-specified Sequences.

Uses of RecyclableSequenceEnumerator in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery with parameters of type RecyclableSequenceEnumerator

Modifier and Type	Method and Description
static Sequence[]	MutableMotifDiscovererToolbox.enumerate(DifferentiableSequenceScore[] funs, int[] classIndex, int[] motifIndex, RecyclableSequenceEnumerator[] rse, double weight, DiffSSBasedOptimizableFunction opt, OutputStream out) This method allows to enumerate all possible seeds for a number of motifs in the MutableMotifDiscoverers of a specific classes.
static Sequence	MutableMotifDiscovererToolbox.enumerate(DifferentiableSequenceScore[] funs, int classIndex, int motifIndex, RecyclableSequenceEnumerator rse, double weight, DiffSSBasedOptimizableFunction opt, OutputStream out) This method allows to enumerate all possible seeds for a motif in the MutableMotifDiscoverer of a specific class.