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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 | |
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static class |
StrandedLocatedSequenceAnnotationWithLength.Strand
This enum defines possible orientations on the strands. |
Field Summary |
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Fields inherited from class de.jstacs.results.ResultSet |
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results |
Constructor Summary | |
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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)
given as a Collection of Result s results . |
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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)
given as an array of Result s results . |
|
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 , additional
annotation (that does not fit the SequenceAnnotation definitions)
given as an array of Result s additionalAnnotations
and sub-annotations annotations . |
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StrandedLocatedSequenceAnnotationWithLength(StringBuffer representation)
The standard constructor for the interface Storable . |
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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 Result s additionalAnnotations
and sub-annotations annotations . |
Method Summary | |
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protected void |
fromXML(StringBuffer representation)
Parses the contents of a ResultSet from its XML representation as
returned by ResultSet.toXML() . |
StrandedLocatedSequenceAnnotationWithLength.Strand |
getStrandedness()
Returns the strandedness, i.e the orientation of this annotation. |
String |
toString()
|
StringBuffer |
toXML()
This method returns an XML representation as StringBuffer of an
instance of the implementing class. |
Methods inherited from class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength |
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getEnd, getLength, overlaps |
Methods inherited from class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation |
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getPosition |
Methods inherited from class de.jstacs.data.sequences.annotation.SequenceAnnotation |
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getAnnotations, getIdentifier, getSubAnnotations, getType |
Methods inherited from class de.jstacs.results.ResultSet |
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findColumn, getNumberOfResults, getResultAt, getResultForName, getResults |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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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)
given as an array of Result
s results
.
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 annotationLocatedSequenceAnnotationWithLength.LocatedSequenceAnnotationWithLength(int,
int, String, String, Result...)
public 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)
given as a Collection
of Result
s results
.
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 annotationLocatedSequenceAnnotationWithLength.LocatedSequenceAnnotationWithLength(int,
int, String, String, Collection)
public StrandedLocatedSequenceAnnotationWithLength(int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotations)
StrandedLocatedSequenceAnnotationWithLength
of type
type
with identifier identifier
, additional
annotation (that does not fit the SequenceAnnotation
definitions)
given as an array of Result
s additionalAnnotations
and sub-annotations 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 annotationLocatedSequenceAnnotationWithLength.LocatedSequenceAnnotationWithLength(int,
int, String, String, SequenceAnnotation[], Result...)
public StrandedLocatedSequenceAnnotationWithLength(String type, String identifier, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotations)
StrandedLocatedSequenceAnnotationWithLength
of type
type
with identifier identifier
, additional
annotation (that does not fit the SequenceAnnotation
definitions)
given as an array of Result
s additionalAnnotations
and sub-annotations annotations
. The position of the new
LocatedSequenceAnnotationWithLength
is the minimal position of
all positions of annotations
and the length is determined so
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 annotationLocatedSequenceAnnotationWithLength.LocatedSequenceAnnotationWithLength(String,
String, LocatedSequenceAnnotation[], Result...)
,
LocatedSequenceAnnotationWithLength.getEnd()
public StrandedLocatedSequenceAnnotationWithLength(StringBuffer representation) throws NonParsableException
Storable
.
Creates a new StrandedLocatedSequenceAnnotationWithLength
out of
its XML representation.
representation
- the XML representation as StringBuffer
NonParsableException
- if the StrandedLocatedSequenceAnnotationWithLength
could not be reconstructed out of the XML representation (the
StringBuffer
representation
could not be
parsed)LocatedSequenceAnnotationWithLength.LocatedSequenceAnnotationWithLength(StringBuffer)
,
Storable
Method Detail |
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public StrandedLocatedSequenceAnnotationWithLength.Strand 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 as StringBuffer
NonParsableException
- if the XML code could not be parsedpublic String toString()
toString
in class LocatedSequenceAnnotationWithLength
public StringBuffer toXML()
Storable
StringBuffer
of an
instance of the implementing class.
toXML
in interface Storable
toXML
in class LocatedSequenceAnnotationWithLength
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