public class SequenceAnnotation extends ResultSet
Sequence
.
Annotations may be e.g. exons, introns, coding sequences or splice sites.Constructor and Description |
---|
SequenceAnnotation(StringBuffer representation)
The standard constructor for the interface
Storable . |
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 . |
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 . |
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 . |
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 . |
Modifier and Type | Method and Description |
---|---|
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. |
int |
hashCode() |
String |
toString() |
StringBuffer |
toXML()
This method returns an XML representation as
StringBuffer of an
instance of the implementing class. |
findColumn, getNumberOfResults, getResultAt, getResultForName, getResults
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
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
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.public String getIdentifier()
SequenceAnnotation
as given in the
constructor.SequenceAnnotation