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Packages that use RecyclableSequenceEnumerator | |
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de.jstacs.data | Provides classes for the representation of data. |
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer |
Uses of RecyclableSequenceEnumerator in de.jstacs.data |
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Classes in de.jstacs.data that implement RecyclableSequenceEnumerator | |
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class |
DiscreteSequenceEnumerator
This class enumerates over all Sequence s of a specific
AlphabetContainer and length. |
static class |
Sample.ElementEnumerator
This class can be used to have a fast sequential access to a Sample . |
class |
SampleKMerEnumerator
Class for an RecyclableSequenceEnumerator of Sequence s that enumerates all k-mers that exist in a given Sample , optionally ignoring reverse complements. |
class |
SequenceEnumeration
This class implements a RecyclableSequenceEnumerator on user-specified Sequence s. |
Uses of RecyclableSequenceEnumerator in de.jstacs.motifDiscovery |
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Methods in de.jstacs.motifDiscovery with parameters of type RecyclableSequenceEnumerator | |
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static Sequence[] |
MutableMotifDiscovererToolbox.enumerate(ScoringFunction[] funs,
int[] classIndex,
int[] motifIndex,
RecyclableSequenceEnumerator[] rse,
double weight,
SFBasedOptimizableFunction opt,
OutputStream out)
This method allows to enumerate all possible seeds for a number of motifs in the MutableMotifDiscoverer s of a specific classes. |
static Sequence |
MutableMotifDiscovererToolbox.enumerate(ScoringFunction[] funs,
int classIndex,
int motifIndex,
RecyclableSequenceEnumerator rse,
double weight,
SFBasedOptimizableFunction opt,
OutputStream out)
This method allows to enumerate all possible seeds for a motif in the MutableMotifDiscoverer of a specific class. |
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