Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES

## Uses of Class
de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength.Strand

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)`

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES