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java.lang.Objectde.jstacs.results.ResultSet
de.jstacs.data.sequences.annotation.SequenceAnnotation
de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation
public class LocatedSequenceAnnotation
Class for a SequenceAnnotation
that has a position on the sequence, e.g for transcription start sites or intron-exon junctions.
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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LocatedSequenceAnnotation(int position,
String type,
String identifier,
Collection<Result> results)
Creates a new LocatedSequenceAnnotation of type type , with identifier identifier , and additional annotation (that does not fit the SequenceAnnotation definitions)
result . |
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LocatedSequenceAnnotation(int position,
String type,
String identifier,
Result... results)
Creates a new LocatedSequenceAnnotation of type type , with identifier identifier , and additional annotation (that does not fit the SequenceAnnotation definitions)
result . |
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LocatedSequenceAnnotation(int position,
String type,
String identifier,
SequenceAnnotation[] annotations,
Result... additionalAnnotation)
Creates a new LocatedSequenceAnnotation of type type , with identifier identifier , additional annotation (that does not fit the SequenceAnnotation definitions)
result , and sub annotations. |
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LocatedSequenceAnnotation(StringBuffer representation)
Re-creates a LocatedSequenceAnnotation from its XML-representation as returned by toXML() . |
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LocatedSequenceAnnotation(String type,
String identifier,
LocatedSequenceAnnotation[] annotations,
Result... additionalAnnotation)
Creates a new LocatedSequenceAnnotation 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 |
getPosition()
Returns the position of this LocatedSequenceAnnotation on the sequence. |
String |
toString()
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StringBuffer |
toXML()
This method returns an XML-representation of an instance of the implementing class. |
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 LocatedSequenceAnnotation(int position, String type, String identifier, Result... results)
LocatedSequenceAnnotation
of type type
, with identifier identifier
, and additional annotation (that does not fit the SequenceAnnotation
definitions)
result
.
position
- the position of the LocatedSequenceAnnotation
on the sequencetype
- the type of the annotationidentifier
- the identifier of the annotationresults
- the additional annotationpublic LocatedSequenceAnnotation(int position, String type, String identifier, Collection<Result> results)
LocatedSequenceAnnotation
of type type
, with identifier identifier
, and additional annotation (that does not fit the SequenceAnnotation
definitions)
result
.
position
- the position of the LocatedSequenceAnnotation
on the sequencetype
- the type of the annotationidentifier
- the identifier of the annotationresults
- the additional annotationpublic LocatedSequenceAnnotation(int position, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotation)
LocatedSequenceAnnotation
of type type
, with identifier identifier
, additional annotation (that does not fit the SequenceAnnotation
definitions)
result
, and sub annotations.
position
- the position of the LocatedSequenceAnnotation
on the sequencetype
- the type of the annotationidentifier
- the identifier of the annotationannotations
- the sub-annotationsadditionalAnnotation
- the additional annotationpublic LocatedSequenceAnnotation(String type, String identifier, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotation)
LocatedSequenceAnnotation
of type type
, with identifier identifier
, additional annotation (that does not fit the SequenceAnnotation
definitions)
result
, and sub annotations. The position of this LocatedSequenceAnnotation
is the minimum of the positions of annotations
.,
type
- the type of the annotationidentifier
- the identifier of the annotationannotations
- the sub-annotationsadditionalAnnotation
- the additional annotationpublic LocatedSequenceAnnotation(StringBuffer representation) throws NonParsableException
LocatedSequenceAnnotation
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 SequenceAnnotation
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 SequenceAnnotation
public int getPosition()
LocatedSequenceAnnotation
on the sequence.
public String toString()
toString
in class SequenceAnnotation
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