|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava.bio.seq.io.SequenceBuilderFilter
org.biojava.bio.seq.io.EmblProcessor
public class EmblProcessor
Simple filter which handles attribute lines from an EMBL file. This
class delegates creation of Feature
s to a
FeatureTableParser
, which in turn delegates creation
of Locations
to an EmblLikeLocationParser
which is shared with the GenbankProcessor
.
An EmblLikeLocationParser
parses EMBL/Genbank style
locations. Supported location forms:
123 <123 or >123 (123.567) (123.567)..789 123..(567.789) (123.345)..(567.789) 123..456 <123..567 or 123..>567 or <123..>567 123^567 AL123465:(123..567)The only EMBL header information retained over a read/write cycle is the accession number (all numbers).
Nested Class Summary | |
---|---|
static class |
EmblProcessor.Factory
Deprecated. Factory which wraps SequenceBuilders in an EmblProcessor |
Field Summary | |
---|---|
static java.lang.String |
PROPERTY_EMBL_ACCESSIONS
Deprecated. |
Constructor Summary | |
---|---|
EmblProcessor(SequenceBuilder delegate)
Deprecated. |
Method Summary | |
---|---|
void |
addParseErrorListener(ParseErrorListener theListener)
Deprecated. Adds a parse error listener to the list of listeners if it isn't already included. |
void |
addSequenceProperty(java.lang.Object key,
java.lang.Object value)
Deprecated. Notify the listener of a sequence-wide property. |
void |
endSequence()
Deprecated. Notify the listener that processing of the sequence is complete. |
protected void |
notifyParseErrorEvent(ParseErrorEvent theEvent)
Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents. |
void |
removeParseErrorListener(ParseErrorListener theListener)
Deprecated. Removes a parse error listener from the list of listeners if it is included. |
Methods inherited from class org.biojava.bio.seq.io.SequenceBuilderFilter |
---|
addFeatureProperty, addSymbols, endFeature, getDelegate, makeSequence, setName, setURI, startFeature, startSequence |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
public static final java.lang.String PROPERTY_EMBL_ACCESSIONS
Constructor Detail |
---|
public EmblProcessor(SequenceBuilder delegate)
Method Detail |
---|
public void endSequence() throws ParseException
SeqIOListener
endSequence
in interface SeqIOListener
endSequence
in class SequenceBuilderFilter
ParseException
public void addSequenceProperty(java.lang.Object key, java.lang.Object value) throws ParseException
SeqIOListener
addSequenceProperty
in interface SeqIOListener
addSequenceProperty
in class SequenceBuilderFilter
ParseException
public void addParseErrorListener(ParseErrorListener theListener)
addParseErrorListener
in interface ParseErrorSource
theListener
- Listener to be added.public void removeParseErrorListener(ParseErrorListener theListener)
removeParseErrorListener
in interface ParseErrorSource
theListener
- Listener to be removed.protected void notifyParseErrorEvent(ParseErrorEvent theEvent)
theEvent
- The event to be handed to the listeners.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |