public class ReferenceSequenceAnnotation extends SequenceAnnotation
SequenceAnnotation
that contains a reference
sequence. This sequence can be obtained using the method
getReferenceSequence()
.Modifier and Type | Field and Description |
---|---|
static String |
TYPE
The type of a
ReferenceSequenceAnnotation . |
Constructor and Description |
---|
ReferenceSequenceAnnotation(StringBuffer representation)
The standard constructor for the interface
Storable . |
ReferenceSequenceAnnotation(String identifier,
Sequence ref,
Result... results)
Creates a new
ReferenceSequenceAnnotation with identifier
identifier , reference sequence ref , and
additional annotation (that does not fit the SequenceAnnotation
definitions) given as a Result result . |
Modifier and Type | Method and Description |
---|---|
Sequence |
getReferenceSequence()
Returns the reference sequence.
|
int |
hashCode() |
String |
toString() |
StringBuffer |
toXML()
This method returns an XML representation as
StringBuffer of an
instance of the implementing class. |
fromXML, getAnnotations, getIdentifier, getSubAnnotations, getType
findColumn, getNumberOfResults, getResultAt, getResultForName, getResults
public static final String TYPE
ReferenceSequenceAnnotation
.public ReferenceSequenceAnnotation(String identifier, Sequence ref, Result... results)
ReferenceSequenceAnnotation
with identifier
identifier
, reference sequence ref
, and
additional annotation (that does not fit the SequenceAnnotation
definitions) given as a Result
result
.identifier
- the identifier of the annotationref
- the reference sequenceresults
- the additional annotationResultSet.ResultSet(Result)
public ReferenceSequenceAnnotation(StringBuffer representation) throws NonParsableException
Storable
.
Creates a new ReferenceSequenceAnnotation
out of its XML representation.representation
- the XML representation as StringBuffer
NonParsableException
- if the ReferenceSequenceAnnotation
could not be reconstructed
out of the XML representation (the StringBuffer
representation
could not be parsed)SequenceAnnotation.SequenceAnnotation(StringBuffer)
,
Storable
public StringBuffer toXML()
Storable
StringBuffer
of an
instance of the implementing class.toXML
in interface Storable
toXML
in class SequenceAnnotation
public String toString()
toString
in class SequenceAnnotation
public Sequence getReferenceSequence()
public int hashCode()
hashCode
in class SequenceAnnotation