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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)
Re-creates a SequenceAnnotation from its XML-representation as returned by toXML() . |
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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)
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)
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)
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)
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()
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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.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 SequenceAnnotation(String type, String identifier, Result result)
SequenceAnnotation
of type type
, with identifier identifier
, and additional annotation (that does not fit the SequenceAnnotation
definitions)
result
.
type
- the type of the annotationidentifier
- the identifier of the annotationresult
- the additional annotationpublic SequenceAnnotation(String type, String identifier, Result[]... results)
SequenceAnnotation
of type type
, with identifier identifier
, and additional annotation (that does not fit the SequenceAnnotation
definitions)
results
.
type
- the type of the annotationidentifier
- the identifier of the annotationresults
- the additional annotationpublic 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)
additionalAnnotation
. This SequenceAnnotation
may contain sub-annotations, this may be e.g. the donor and acceptor site for splice sites or the exons of for a gene.
type
- the type of the annotationidentifier
- the identifier of the annotationsubAnnotations
- the sub-annotationadditionalAnnotation
- the additional annotationpublic 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)
results
.
type
- the type of the annotationidentifier
- the identifier of the annotationresults
- the additional annotationpublic SequenceAnnotation(StringBuffer representation) throws NonParsableException
SequenceAnnotation
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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public String getType()
SequenceAnnotation
as given in the constructor
public Result[] getAnnotations()
SequenceAnnotation
as given in the constructor.
public SequenceAnnotation[] getSubAnnotations()
SequenceAnnotation
as given in the constructor.
SequenceAnnotation(String, String, SequenceAnnotation[], Result...)
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
NonParsableException
- is thrown if the XML-code could not be parsedpublic StringBuffer toXML()
Storable
toXML
in interface Storable
toXML
in class ResultSet
public String getIdentifier()
SequenceAnnotation
as given in the constructor.
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