public class MotifAnnotation extends StrandedLocatedSequenceAnnotationWithLength
StrandedLocatedSequenceAnnotationWithLength that is a
motif. The usefulness of this class amounts to having a defined type for all
motifs.StrandedLocatedSequenceAnnotationWithLength.Strand| Constructor and Description |
|---|
MotifAnnotation(StringBuffer representation)
The standard constructor for the interface
Storable. |
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
Results additionalAnnotation. |
fromXML, getStrandedness, toString, toXMLgetEnd, getLength, overlapsgetPositiongetAnnotations, getIdentifier, getSubAnnotations, getType, hashCodefindColumn, getNumberOfResults, getResultAt, getResultForName, getResultspublic MotifAnnotation(String identifier, int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, Result... additionalAnnotation)
MotifAnnotation of type type with
identifier identifier and additional annotation (that does
not fit the SequenceAnnotation definitions) given as an array of
Results additionalAnnotation. The orientation of the
motif on the strand is also considered by the value
strandedness of the enum StrandedLocatedSequenceAnnotationWithLength.Strand.position - the position of the
StrandedLocatedSequenceAnnotationWithLength on the
sequencelength - the length of the
StrandedLocatedSequenceAnnotationWithLengthstrandedness - the orientation on the strandidentifier - the identifier of the annotationadditionalAnnotation - the additional annotationStrandedLocatedSequenceAnnotationWithLength.Strand,
StrandedLocatedSequenceAnnotationWithLength.StrandedLocatedSequenceAnnotationWithLength(int,
int, StrandedLocatedSequenceAnnotationWithLength.Strand, String, String, Result[])public MotifAnnotation(StringBuffer representation) throws NonParsableException
Storable.
Creates a new MotifAnnotation out of its XML representation.representation - the XML representation as StringBufferNonParsableException - if the MotifAnnotation could not be reconstructed out
of the XML representation (the StringBuffer
representation could not be parsed)StrandedLocatedSequenceAnnotationWithLength.StrandedLocatedSequenceAnnotationWithLength(StringBuffer),
Storable