|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectde.jstacs.results.ResultSet
de.jstacs.data.sequences.annotation.SequenceAnnotation
de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation
de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength
de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength
public class StrandedLocatedSequenceAnnotationWithLength
Class for a SequenceAnnotation
that has a position, a length, and an orientation on the strand of a Sequence
.
Nested Class Summary | |
---|---|
static class |
StrandedLocatedSequenceAnnotationWithLength.Strand
The possible orientations on the strands. |
Field Summary |
---|
Fields inherited from class de.jstacs.results.ResultSet |
---|
results |
Constructor Summary | |
---|---|
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)
result . |
|
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)
result . |
|
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 , and additional annotation
(that does not fit the SequenceAnnotation definitions)
additionalAnnotations , and sub-annotations. |
|
StrandedLocatedSequenceAnnotationWithLength(StringBuffer representation)
Re-creates a StrandedLocatedSequenceAnnotationWithLength from its XML-representation as returned by toXML() . |
|
StrandedLocatedSequenceAnnotationWithLength(String type,
String identifier,
StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
LocatedSequenceAnnotation[] annotations,
Result... additionalAnnotations)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type type , with identifier identifier , and additional annotation
(that does not fit the SequenceAnnotation definitions)
additionalAnnotations , and sub-annotations. |
Method Summary | |
---|---|
protected void |
fromXML(StringBuffer representation)
Parses the contents of a ResultSet from its XML-representation as returned by ResultSet.toXML() . |
String |
getStrandedness()
Returns the orientation/strandedness of this annotation. |
String |
toString()
|
StringBuffer |
toXML()
This method returns an XML-representation of an instance of the implementing class. |
Methods inherited from class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength |
---|
getEnd, getLength |
Methods inherited from class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation |
---|
getPosition |
Methods inherited from class de.jstacs.data.sequences.annotation.SequenceAnnotation |
---|
getAnnotations, getIdentifier, getSubAnnotations, getType |
Methods inherited from class de.jstacs.results.ResultSet |
---|
findColumn, getNumberOfResults, getResultAt, getResults |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
---|
public StrandedLocatedSequenceAnnotationWithLength(int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, String type, String identifier, Result... results)
StrandedLocatedSequenceAnnotationWithLength
of type type
, with identifier identifier
, and additional annotation
(that does not fit the SequenceAnnotation
definitions)
result
.
position
- the position of the StrandedLocatedSequenceAnnotationWithLength
on the sequencelength
- the length of the StrandedLocatedSequenceAnnotationWithLength
strandedness
- the orientation on the strandtype
- the type of the annotationidentifier
- the identifier of the annotationresults
- the additional annotationpublic StrandedLocatedSequenceAnnotationWithLength(int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, String type, String identifier, Collection<Result> results)
StrandedLocatedSequenceAnnotationWithLength
of type type
, with identifier identifier
, and additional annotation
(that does not fit the SequenceAnnotation
definitions)
result
.
position
- the position of the StrandedLocatedSequenceAnnotationWithLength
on the sequencelength
- the length of the StrandedLocatedSequenceAnnotationWithLength
strandedness
- the orientation on the strandtype
- the type of the annotationidentifier
- the identifier of the annotationresults
- the additional annotationpublic StrandedLocatedSequenceAnnotationWithLength(int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotations)
StrandedLocatedSequenceAnnotationWithLength
of type type
, with identifier identifier
, and additional annotation
(that does not fit the SequenceAnnotation
definitions)
additionalAnnotations
, and sub-annotations.
position
- the position of the StrandedLocatedSequenceAnnotationWithLength
on the sequencelength
- the length of the StrandedLocatedSequenceAnnotationWithLength
strandedness
- the orientation on the strandtype
- the type of the annotationidentifier
- the identifier of the annotationannotations
- the sub-annotationsadditionalAnnotations
- the additional annotationpublic StrandedLocatedSequenceAnnotationWithLength(String type, String identifier, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotations)
StrandedLocatedSequenceAnnotationWithLength
of type type
, with identifier identifier
, and additional annotation
(that does not fit the SequenceAnnotation
definitions)
additionalAnnotations
, and sub-annotations. The position of the new LocatedSequenceAnnotationWithLength
is the minimal position of all positions
of annotations
and the length is determined such that it is the maximum of these positions and (if applicable) the corresponding
values of LocatedSequenceAnnotationWithLength.getEnd()
.
strandedness
- the orientation on the strandtype
- the type of the annotationidentifier
- the identifier of the annotationannotations
- the sub-annotationsadditionalAnnotations
- the additional annotationpublic StrandedLocatedSequenceAnnotationWithLength(StringBuffer representation) throws NonParsableException
StrandedLocatedSequenceAnnotationWithLength
from its XML-representation as returned by toXML()
.
representation
- the XML-representation
NonParsableException
- is thrown if the XML-code could not be parsedMethod Detail |
---|
public String getStrandedness()
protected void fromXML(StringBuffer representation) throws NonParsableException
ResultSet
ResultSet
from its XML-representation as returned by ResultSet.toXML()
.
fromXML
in class LocatedSequenceAnnotationWithLength
representation
- the XML-representation
NonParsableException
- is thrown if the XML-code could not be parsedpublic String toString()
toString
in class LocatedSequenceAnnotationWithLength
public StringBuffer toXML()
Storable
toXML
in interface Storable
toXML
in class LocatedSequenceAnnotationWithLength
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |