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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) given as a
Collection of Result s 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) given as an
array of Result s 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) given as an array of
Result s additionalAnnotation and sub-annotations
annotations . |
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LocatedSequenceAnnotation(StringBuffer representation)
The standard constructor for the interface Storable . |
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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) given as an array of
Result s additionalAnnotation 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() . |
int |
getPosition()
Returns the position of this LocatedSequenceAnnotation on the
sequence. |
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.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 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) given as an
array of Result
s result
.
position
- the position of the LocatedSequenceAnnotation
on the
sequencetype
- the type of the annotationidentifier
- the identifier of the annotationresults
- the additional annotationSequenceAnnotation.SequenceAnnotation(String, String, Result[][])
public 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) given as a
Collection
of Result
s result
.
position
- the position of the LocatedSequenceAnnotation
on the
sequencetype
- the type of the annotationidentifier
- the identifier of the annotationresults
- the additional annotationSequenceAnnotation.SequenceAnnotation(String, String, Collection)
public 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) given as an array of
Result
s additionalAnnotation
and sub-annotations
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 annotationSequenceAnnotation.SequenceAnnotation(String, String,
SequenceAnnotation[], Result...)
public 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) given as an array of
Result
s additionalAnnotation
and sub-annotations
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 annotationSequenceAnnotation.SequenceAnnotation(String, String,
SequenceAnnotation[], Result...)
public LocatedSequenceAnnotation(StringBuffer representation) throws NonParsableException
Storable
.
Creates a new LocatedSequenceAnnotation
out of its XML
representation.
representation
- the XML representation as StringBuffer
NonParsableException
- if the LocatedSequenceAnnotation
could not be
reconstructed out of the XML representation (the
StringBuffer
representation
could not be
parsed)SequenceAnnotation.SequenceAnnotation(StringBuffer)
,
Storable
Method 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 as StringBuffer
NonParsableException
- if the XML code could not be parsedpublic StringBuffer toXML()
Storable
StringBuffer
of an
instance of the implementing class.
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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