de.jstacs.data.sequences.annotation
Class ReferenceSequenceAnnotation
java.lang.Object
de.jstacs.results.ResultSet
de.jstacs.data.sequences.annotation.SequenceAnnotation
de.jstacs.data.sequences.annotation.ReferenceSequenceAnnotation
- All Implemented Interfaces:
- Storable
public class ReferenceSequenceAnnotation
- extends SequenceAnnotation
This class implements a SequenceAnnotation
that contains a reference
sequence. This sequence can be obtained using the method
getReferenceSequence()
.
- Author:
- Jan Grau
TYPE
public static final String TYPE
- The type of a
ReferenceSequenceAnnotation
.
- See Also:
SequenceAnnotation.getType()
,
Constant Field Values
ReferenceSequenceAnnotation
public 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
.
- Parameters:
identifier
- the identifier of the annotationref
- the reference sequenceresults
- the additional annotation- See Also:
ResultSet.ResultSet(Result)
ReferenceSequenceAnnotation
public ReferenceSequenceAnnotation(StringBuffer representation)
throws NonParsableException
- The standard constructor for the interface
Storable
.
Creates a new ReferenceSequenceAnnotation
out of its XML representation.
- Parameters:
representation
- the XML representation as StringBuffer
- Throws:
NonParsableException
- if the ReferenceSequenceAnnotation
could not be reconstructed
out of the XML representation (the StringBuffer
representation
could not be parsed)- See Also:
SequenceAnnotation.SequenceAnnotation(StringBuffer)
,
Storable
toXML
public StringBuffer toXML()
- Description copied from interface:
Storable
- This method returns an XML representation as
StringBuffer
of an
instance of the implementing class.
- Specified by:
toXML
in interface Storable
- Overrides:
toXML
in class SequenceAnnotation
- Returns:
- the XML representation
toString
public String toString()
- Overrides:
toString
in class SequenceAnnotation
getReferenceSequence
public Sequence getReferenceSequence()
- Returns the reference sequence.
- Returns:
- the reference sequence