public interface RichSeqIOListener extends SeqIOListener
Modifier and Type | Method and Description |
---|---|
RichFeature |
getCurrentFeature()
Gets the feature currently being created.
|
void |
setAccession(String accession)
Call back method so the event emitter can tell the listener
the accession of the record being read.
|
void |
setCircular(boolean circular)
Defined this sequence being parser as circular.
|
void |
setComment(String comment)
Call back method so the event emitter can tell the listener
about a comment in the record being read.
|
void |
setDescription(String description)
Call back method so the event emitter can tell the listener
the description of the record being read.
|
void |
setDivision(String division)
Call back method so the event emitter can tell the listener
the division of the record being read.
|
void |
setIdentifier(String identifier)
Call back method so the event emitter can tell the listener
the identifier of the record being read.
|
void |
setNamespace(Namespace namespace)
Call back method so the event emitter can tell the listener
the namespace of the record being read.
|
void |
setRankedCrossRef(RankedCrossRef crossRef)
Call back method so the event emitter can tell the listener about a cross reference.
|
void |
setRankedDocRef(RankedDocRef ref)
Call back method so the event emitter can tell the listener
about a literature reference in the record being read.
|
void |
setRelationship(BioEntryRelationship relationship)
Call back method so the event emitter can tell the listener
about a relationship between the bioentry or sequence in the
record being read and another bioentry.
|
void |
setSeqVersion(String version)
Call back method so the event emitter can tell the listener
the version of the sequence of the record being read.
|
void |
setTaxon(NCBITaxon taxon)
Call back method so the event emitter can tell the listener
the Taxon of the record being read.
|
void |
setURI(String uri)
Deprecated.
There is no clear mapping between URI and BioSQL. This
method is no longer used or supported in biojavax. Don't use it. Calling
it may result in exceptions. Use instead setName(String name),
setAccession(String accession), setVersion(int version) etc as
appropriate.
|
void |
setVersion(int version)
Call back method so the event emitter can tell the listener
the version of the record being read.
|
addFeatureProperty, addSequenceProperty, addSymbols, endFeature, endSequence, setName, startFeature, startSequence
void setAccession(String accession) throws ParseException
accession
- The accession of the recordParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.SeqIOListener.setName(String name)
,
setURI(String uri)
,
setIdentifier(String identifier)
void setIdentifier(String identifier) throws ParseException
identifier
- The identifier of the Bioentry.ParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.SeqIOListener.setName(String name)
,
setAccession(String accession)
,
setURI(String uri)
void setDivision(String division) throws ParseException
division
- The division the entry belongs too.ParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.void setDescription(String description) throws ParseException
description
- The description of the recordParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.void setVersion(int version) throws ParseException
version
- the version of the recordParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.void setSeqVersion(String version) throws ParseException
version
- the version of the recordParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.void setComment(String comment) throws ParseException
comment
- The commentParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.void setRankedDocRef(RankedDocRef ref) throws ParseException
ref
- A literature reference contained in the entry.ParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.void setTaxon(NCBITaxon taxon) throws ParseException
taxon
- The taxon information relevant to this entry.ParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.void setNamespace(Namespace namespace) throws ParseException
The namespace is a concept from the BioSQL schema that enables Bioentries to be disambiguated. It is possible in BioSQL and should be possible in other collections of BioEntries to have records that have the same name, accession and version but different namespaces. This method would be expected to be called if you are reading a sequence from a biosql database or if you are implementing a listener that knows how to write to a biosql database. If you give a sequence a namespace and it is persited to biosql at somepoint in it's life you could expect it to be persisted to that namespace (if possible).
namespace
- The namespace of the entry.ParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.void setRelationship(BioEntryRelationship relationship) throws ParseException
relationship
- The relationshipParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.void setRankedCrossRef(RankedCrossRef crossRef) throws ParseException
crossRef
- the cross referenceParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.void setURI(String uri) throws ParseException
setURI
in interface SeqIOListener
ParseException
RichFeature getCurrentFeature() throws ParseException
ParseException
- if a feature is not currently being created.void setCircular(boolean circular) throws ParseException
circular
- set this to true if you want it to be circular.ParseException
- If the Listener cannot understand the event, is unable
to deal with the event or is not expecting the event.Copyright © 2020 BioJava. All rights reserved.