Package | Description |
---|---|
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. |
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
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 |
Constructor and Description |
---|
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 . |
Modifier and Type | Method and Description |
---|---|
StrandedLocatedSequenceAnnotationWithLength.Strand |
NormalizedDiffSM.getStrand(Sequence seq,
int startPos)
This method return the preferred
StrandedLocatedSequenceAnnotationWithLength.Strand for a Sequence beginning at startPos . |
Modifier and Type | Method and Description |
---|---|
StrandedLocatedSequenceAnnotationWithLength.Strand |
StrandDiffSM.getStrand(Sequence seq,
int startPos)
This method returns the preferred
StrandedLocatedSequenceAnnotationWithLength.Strand for a given subsequence. |