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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
public class LocatedSequenceAnnotationWithLength
Class for a SequenceAnnotation
that has a position on the sequence and a length, e.g. for donor splice sites, exons, or genes.
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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LocatedSequenceAnnotationWithLength(int position,
int length,
String type,
String identifier,
Collection<Result> results)
Creates a new LocatedSequenceAnnotationWithLength of type type , with identifier identifier , and additional annotation
(that does not fit the SequenceAnnotation definitions)
result . |
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LocatedSequenceAnnotationWithLength(int position,
int length,
String type,
String identifier,
Result... results)
Creates a new LocatedSequenceAnnotationWithLength of type type , with identifier identifier , and additional annotation
(that does not fit the SequenceAnnotation definitions)
result . |
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LocatedSequenceAnnotationWithLength(int position,
int length,
String type,
String identifier,
SequenceAnnotation[] annotations,
Result... additionalAnnotations)
Creates a new LocatedSequenceAnnotationWithLength of type type , with identifier identifier , additional annotation
(that does not fit the SequenceAnnotation definitions)
result , and sub-annotations. |
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LocatedSequenceAnnotationWithLength(StringBuffer representation)
Re-creates a LocatedSequenceAnnotationWithLength from its XML-representation as returned by toXML() . |
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LocatedSequenceAnnotationWithLength(String type,
String identifier,
LocatedSequenceAnnotation[] annotations,
Result... additionalAnnotations)
Creates a new LocatedSequenceAnnotationWithLength of type type , with identifier identifier , additional annotation
(that does not fit the SequenceAnnotation definitions)
result , and sub-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() . |
int |
getEnd()
Returns the end of this LocatedSequenceAnnotationWithLength , i.e. |
int |
getLength()
Returns the length of this LocatedSequenceAnnotationWithLength as given in the constructor. |
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.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, 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 LocatedSequenceAnnotationWithLength(int position, int length, String type, String identifier, Result... results)
LocatedSequenceAnnotationWithLength
of type type
, with identifier identifier
, and additional annotation
(that does not fit the SequenceAnnotation
definitions)
result
.
position
- the position of the LocatedSequenceAnnotationWithLength
on the sequencelength
- the length of the LocatedSequenceAnnotationWithLength
type
- the type of the annotationidentifier
- the identifier of the annotationresults
- the additional annotationpublic LocatedSequenceAnnotationWithLength(int position, int length, String type, String identifier, Collection<Result> results)
LocatedSequenceAnnotationWithLength
of type type
, with identifier identifier
, and additional annotation
(that does not fit the SequenceAnnotation
definitions)
result
.
position
- the position of the LocatedSequenceAnnotationWithLength
on the sequencelength
- the length of the LocatedSequenceAnnotationWithLength
type
- the type of the annotationidentifier
- the identifier of the annotationresults
- the additional annotationpublic LocatedSequenceAnnotationWithLength(int position, int length, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotations)
LocatedSequenceAnnotationWithLength
of type type
, with identifier identifier
, additional annotation
(that does not fit the SequenceAnnotation
definitions)
result
, and sub-annotations.
position
- the position of the LocatedSequenceAnnotationWithLength
on the sequencelength
- the length of the LocatedSequenceAnnotationWithLength
type
- the type of the annotationidentifier
- the identifier of the annotationannotations
- the sub-annotationsadditionalAnnotations
- the additional annotationpublic LocatedSequenceAnnotationWithLength(String type, String identifier, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotations)
LocatedSequenceAnnotationWithLength
of type type
, with identifier identifier
, additional annotation
(that does not fit the SequenceAnnotation
definitions)
result
, 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 getEnd()
.
type
- the type of the annotationidentifier
- the identifier of the annotationannotations
- the sub-annotationsadditionalAnnotations
- the additional annotationpublic LocatedSequenceAnnotationWithLength(StringBuffer representation) throws NonParsableException
LocatedSequenceAnnotationWithLength
from its XML-representation as returned by toXML()
.
representation
- the XML-representation
NonParsableException
- is thrown if the XML-code could not be parsedMethod Detail |
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protected void fromXML(StringBuffer representation) throws NonParsableException
ResultSet
ResultSet
from its XML-representation as returned by ResultSet.toXML()
.
fromXML
in class LocatedSequenceAnnotation
representation
- the XML-representation
NonParsableException
- is thrown if the XML-code could not be parsedpublic StringBuffer toXML()
Storable
toXML
in interface Storable
toXML
in class LocatedSequenceAnnotation
public int getLength()
LocatedSequenceAnnotationWithLength
as given in the constructor.
public int getEnd()
LocatedSequenceAnnotationWithLength
, i.e.
LocatedSequenceAnnotation.getPosition()
+ getLength()
public String toString()
toString
in class LocatedSequenceAnnotation
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