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java.lang.Objectorg.biojava.bio.seq.io.SequenceBuilderFilter
org.biojava.bio.seq.io.GenbankProcessor
Simple filter which handles attribute lines from a Genbank file
Nested Class Summary | |
static class |
GenbankProcessor.Factory
Factory which wraps sequence builders in a GenbankProcessor |
Field Summary | |
protected FeatureTableParser |
features
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static java.lang.String |
PROPERTY_GENBANK_ACCESSIONS
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Constructor Summary | |
GenbankProcessor(SequenceBuilder theDelegate)
|
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GenbankProcessor(SequenceBuilder theDelegate,
java.lang.String theSource)
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Method Summary | |
void |
addParseErrorListener(ParseErrorListener theListener)
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)
Notify the listener of a sequence-wide property. |
void |
endSequence()
Notify the listener that processing of the sequence is complete. |
protected void |
notifyParseErrorEvent(ParseErrorEvent theEvent)
Passes the event on to all the listeners registered for ParseErrorEvents. |
void |
removeParseErrorListener(ParseErrorListener theListener)
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_GENBANK_ACCESSIONS
protected FeatureTableParser features
Constructor Detail |
public GenbankProcessor(SequenceBuilder theDelegate, java.lang.String theSource)
public GenbankProcessor(SequenceBuilder theDelegate)
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.
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