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java.lang.Objectde.jstacs.results.ResultSet
de.jstacs.data.sequences.annotation.SequenceAnnotation
public class SequenceAnnotation
Class for a general annotation of a Sequence
.
Annotations may be e.g. exons, introns, coding sequences or splice sites.
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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SequenceAnnotation(StringBuffer representation)
The standard constructor for the interface Storable . |
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SequenceAnnotation(String type,
String identifier,
Collection<? extends Result> results)
Creates a new SequenceAnnotation 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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SequenceAnnotation(String type,
String identifier,
Result result)
Creates a new SequenceAnnotation of type type with
identifier identifier and additional annotation (that does
not fit the SequenceAnnotation definitions) given as a
Result result . |
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SequenceAnnotation(String type,
String identifier,
Result[]... results)
Creates a new SequenceAnnotation of type type with
identifier identifier and additional annotation (that does
not fit the SequenceAnnotation definitions) given as an array of
Result s results . |
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SequenceAnnotation(String type,
String identifier,
SequenceAnnotation[] subAnnotations,
Result... additionalAnnotation)
Creates a new SequenceAnnotation of type type with
identifier identifier and additional annotation (that does
not fit the SequenceAnnotation definitions) given as an array of
Result s additionalAnnotation . |
Method Summary | |
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protected void |
fromXML(StringBuffer source)
Parses the contents of a ResultSet from its XML representation as
returned by ResultSet.toXML() . |
Result[] |
getAnnotations()
Returns the additional annotations of this SequenceAnnotation as
given in the constructor. |
String |
getIdentifier()
Returns the identifier of this SequenceAnnotation as given in the
constructor. |
SequenceAnnotation[] |
getSubAnnotations()
Returns the sub-annotations of this SequenceAnnotation as given
in the constructor. |
String |
getType()
Returns the type of this SequenceAnnotation as given in the
constructor. |
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.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 SequenceAnnotation(String type, String identifier, Result result)
SequenceAnnotation
of type type
with
identifier identifier
and additional annotation (that does
not fit the SequenceAnnotation
definitions) given as a
Result
result
.
type
- the type of the annotationidentifier
- the identifier of the annotationresult
- the additional annotationResultSet.ResultSet(Result)
public SequenceAnnotation(String type, String identifier, Result[]... results)
SequenceAnnotation
of type type
with
identifier identifier
and additional annotation (that does
not fit the SequenceAnnotation
definitions) given as an array of
Result
s results
.
type
- the type of the annotationidentifier
- the identifier of the annotationresults
- the additional annotationResultSet.ResultSet(Result[][])
public SequenceAnnotation(String type, String identifier, SequenceAnnotation[] subAnnotations, Result... additionalAnnotation)
SequenceAnnotation
of type type
with
identifier identifier
and additional annotation (that does
not fit the SequenceAnnotation
definitions) given as an array of
Result
s additionalAnnotation
. This
SequenceAnnotation
may contain sub-annotations
subAnnotations
, this may be e.g. the donor and acceptor site
for splice sites or the exons for a gene.
type
- the type of the annotationidentifier
- the identifier of the annotationsubAnnotations
- the sub-annotationadditionalAnnotation
- the additional annotationResultSet.ResultSet(Result[][])
public SequenceAnnotation(String type, String identifier, Collection<? extends Result> results)
SequenceAnnotation
of type type
with
identifier identifier
and additional annotation (that does
not fit the SequenceAnnotation
definitions) given as a
Collection
of Result
s results
.
type
- the type of the annotationidentifier
- the identifier of the annotationresults
- the additional annotationResultSet.ResultSet(Collection)
public SequenceAnnotation(StringBuffer representation) throws NonParsableException
Storable
.
Creates a new SequenceAnnotation
out of its XML representation.
representation
- the XML representation as StringBuffer
NonParsableException
- if the SequenceAnnotation
could not be reconstructed
out of the XML representation (the StringBuffer
representation
could not be parsed)ResultSet.ResultSet(StringBuffer)
,
Storable
Method Detail |
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public String getType()
SequenceAnnotation
as given in the
constructor.
SequenceAnnotation
public Result[] getAnnotations()
SequenceAnnotation
as
given in the constructor.
SequenceAnnotation
public SequenceAnnotation[] getSubAnnotations()
SequenceAnnotation
as given
in the constructor.
SequenceAnnotation
public String toString()
toString
in class ResultSet
protected void fromXML(StringBuffer source) throws NonParsableException
ResultSet
ResultSet
from its XML representation as
returned by ResultSet.toXML()
.
fromXML
in class ResultSet
source
- 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 ResultSet
public String getIdentifier()
SequenceAnnotation
as given in the
constructor.
SequenceAnnotation
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