| Package | Description |
|---|---|
| de.jstacs.data.sequences.annotation |
Provides the facilities to annotate
Sequences using a number of pre-defined annotation types, or additional
implementations of the SequenceAnnotation class. |
| Modifier and Type | Class and Description |
|---|---|
class |
IntronAnnotation
Annotation class for an intron as defined by a donor and an acceptor splice
site.
|
class |
LocatedSequenceAnnotationWithLength
Class for a
SequenceAnnotation that has a position on the sequence
and a length, e.g. |
class |
MotifAnnotation
Class for a
StrandedLocatedSequenceAnnotationWithLength that is a
motif. |
class |
SinglePositionSequenceAnnotation
Class for some annotations that consist mainly of one position on a sequence.
|
class |
StrandedLocatedSequenceAnnotationWithLength
Class for a
SequenceAnnotation that has a position, a length and an
orientation on the strand of a Sequence. |
| Constructor and Description |
|---|
LocatedSequenceAnnotation(String type,
String identifier,
LocatedSequenceAnnotation[] annotations,
Result... additionalAnnotation)
Creates a new
LocatedSequenceAnnotation of type type
with identifier identifier, additional annotation (that does
not fit the SequenceAnnotation definitions) given as an array of
Results additionalAnnotation and sub-annotations
annotations. |
LocatedSequenceAnnotationWithLength(String type,
String identifier,
LocatedSequenceAnnotation[] annotations,
Result... additionalAnnotations)
Creates a new
LocatedSequenceAnnotationWithLength of type
type with identifier identifier, additional
annotation (that does not fit the SequenceAnnotation definitions)
given as an array of Results 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 Results additionalAnnotations
and sub-annotations annotations. |