|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use StrandedLocatedSequenceAnnotationWithLength.Strand | |
---|---|
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.models.mixture.motif | |
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer |
de.jstacs.scoringFunctions | Provides ScoringFunction s that can be used in a ScoreClassifier . |
de.jstacs.scoringFunctions.mix | Provides ScoringFunction s that are mixtures of other ScoringFunction s. |
de.jstacs.scoringFunctions.mix.motifSearch |
Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.data.sequences.annotation |
---|
Methods in de.jstacs.data.sequences.annotation that return StrandedLocatedSequenceAnnotationWithLength.Strand | |
---|---|
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're declared. |
Constructors in de.jstacs.data.sequences.annotation with parameters of type StrandedLocatedSequenceAnnotationWithLength.Strand | |
---|---|
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 . |
|
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 . |
|
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 . |
|
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 . |
|
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.models.mixture.motif |
---|
Methods in de.jstacs.models.mixture.motif that return StrandedLocatedSequenceAnnotationWithLength.Strand | |
---|---|
StrandedLocatedSequenceAnnotationWithLength.Strand |
SingleHiddenMotifMixture.getStrandFor(int component,
int motif,
Sequence sequence,
int startpos)
|
Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.motifDiscovery |
---|
Methods in de.jstacs.motifDiscovery that return StrandedLocatedSequenceAnnotationWithLength.Strand | |
---|---|
StrandedLocatedSequenceAnnotationWithLength.Strand |
MotifDiscoverer.getStrandFor(int component,
int motif,
Sequence sequence,
int startpos)
This method returns the strand for a given subsequence if it is considered as site of the motif model in a specific component. |
Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.scoringFunctions |
---|
Methods in de.jstacs.scoringFunctions that return StrandedLocatedSequenceAnnotationWithLength.Strand | |
---|---|
StrandedLocatedSequenceAnnotationWithLength.Strand |
NormalizedScoringFunction.getStrand(Sequence seq,
int startPos)
This method return the preferred StrandedLocatedSequenceAnnotationWithLength.Strand for a Sequence beginning at startPos . |
StrandedLocatedSequenceAnnotationWithLength.Strand |
IndependentProductScoringFunction.getStrandFor(int component,
int motif,
Sequence sequence,
int startpos)
|
Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.scoringFunctions.mix |
---|
Methods in de.jstacs.scoringFunctions.mix that return StrandedLocatedSequenceAnnotationWithLength.Strand | |
---|---|
StrandedLocatedSequenceAnnotationWithLength.Strand |
StrandScoringFunction.getStrand(Sequence seq,
int startPos)
This method returns the preferred StrandedLocatedSequenceAnnotationWithLength.Strand for a given subsequence. |
Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.scoringFunctions.mix.motifSearch |
---|
Methods in de.jstacs.scoringFunctions.mix.motifSearch that return StrandedLocatedSequenceAnnotationWithLength.Strand | |
---|---|
StrandedLocatedSequenceAnnotationWithLength.Strand |
HiddenMotifsMixture.getStrandFor(int component,
int motif,
Sequence sequence,
int startpos)
|
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |