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Packages that use StrandedLocatedSequenceAnnotationWithLength.Strand | |
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de.jstacs.data.sequences.annotation | Provides the facilities to annotate Sequence s using a number of pre-defined annotation types, or additional
implementations of the SequenceAnnotation class |
de.jstacs.sequenceScores.statisticalModels.differentiable | Provides all DifferentiableStatisticalModel s, which can compute the gradient with
respect to their parameters for a given input Sequence . |
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | Provides DifferentiableSequenceScore s that are mixtures of other DifferentiableSequenceScore s. |
Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.data.sequences.annotation |
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Methods in de.jstacs.data.sequences.annotation that return StrandedLocatedSequenceAnnotationWithLength.Strand | |
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StrandedLocatedSequenceAnnotationWithLength.Strand |
StrandedLocatedSequenceAnnotationWithLength.getStrandedness()
Returns the strandedness, i.e the orientation of this annotation. |
static StrandedLocatedSequenceAnnotationWithLength.Strand |
StrandedLocatedSequenceAnnotationWithLength.Strand.valueOf(String name)
Returns the enum constant of this type with the specified name. |
static StrandedLocatedSequenceAnnotationWithLength.Strand[] |
StrandedLocatedSequenceAnnotationWithLength.Strand.values()
Returns an array containing the constants of this enum type, in the order they are declared. |
Methods in de.jstacs.data.sequences.annotation with parameters of type StrandedLocatedSequenceAnnotationWithLength.Strand | |
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protected void |
MotifAnnotationParser.add(String identifier,
int position,
int length,
StrandedLocatedSequenceAnnotationWithLength.Strand strandedness)
Adds the motif with identifier identifier at position position
with length length and StrandedLocatedSequenceAnnotationWithLength.Strand strandedness |
Constructors in de.jstacs.data.sequences.annotation with parameters of type StrandedLocatedSequenceAnnotationWithLength.Strand | |
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MotifAnnotation(String identifier,
int position,
int length,
StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
Result... additionalAnnotation)
Creates a new MotifAnnotation of type type with
identifier identifier and additional annotation (that does
not fit the SequenceAnnotation definitions) given as an array of
Result s additionalAnnotation . |
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StrandedLocatedSequenceAnnotationWithLength(int position,
int length,
StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
String type,
String identifier,
Collection<Result> results)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type
type with identifier identifier and additional
annotation (that does not fit the SequenceAnnotation definitions)
given as a Collection of Result s results . |
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StrandedLocatedSequenceAnnotationWithLength(int position,
int length,
StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
String type,
String identifier,
Result... results)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type
type with identifier identifier and additional
annotation (that does not fit the SequenceAnnotation definitions)
given as an array of Result s results . |
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StrandedLocatedSequenceAnnotationWithLength(int position,
int length,
StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
String type,
String identifier,
SequenceAnnotation[] annotations,
Result... additionalAnnotations)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type
type with identifier identifier , additional
annotation (that does not fit the SequenceAnnotation definitions)
given as an array of Result s additionalAnnotations
and sub-annotations annotations . |
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StrandedLocatedSequenceAnnotationWithLength(String type,
String identifier,
StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
LocatedSequenceAnnotation[] annotations,
Result... additionalAnnotations)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type
type with identifier identifier , additional
annotation (that does not fit the SequenceAnnotation definitions)
given as an array of Result s additionalAnnotations
and sub-annotations annotations . |
Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.sequenceScores.statisticalModels.differentiable |
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Methods in de.jstacs.sequenceScores.statisticalModels.differentiable that return StrandedLocatedSequenceAnnotationWithLength.Strand | |
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StrandedLocatedSequenceAnnotationWithLength.Strand |
NormalizedDiffSM.getStrand(Sequence seq,
int startPos)
This method return the preferred StrandedLocatedSequenceAnnotationWithLength.Strand for a Sequence beginning at startPos . |
Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture |
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Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture that return StrandedLocatedSequenceAnnotationWithLength.Strand | |
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StrandedLocatedSequenceAnnotationWithLength.Strand |
StrandDiffSM.getStrand(Sequence seq,
int startPos)
This method returns the preferred StrandedLocatedSequenceAnnotationWithLength.Strand for a given subsequence. |
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