org.biojava.bio.seq.io
Class GenbankProcessor

java.lang.Object
  extended byorg.biojava.bio.seq.io.SequenceBuilderFilter
      extended byorg.biojava.bio.seq.io.GenbankProcessor
All Implemented Interfaces:
ParseErrorSource, SeqIOListener, SequenceBuilder
Direct Known Subclasses:
ProteinRefSeqProcessor

public class GenbankProcessor
extends SequenceBuilderFilter
implements ParseErrorSource

Simple filter which handles attribute lines from a Genbank file

Author:
Greg Cox

Nested Class Summary
static class GenbankProcessor.Factory
          Factory which wraps sequence builders in a GenbankProcessor
 
Field Summary
protected  FeatureTableParser features
           
static java.lang.String PROPERTY_GENBANK_ACCESSIONS
           
 
Constructor Summary
GenbankProcessor(SequenceBuilder theDelegate)
           
GenbankProcessor(SequenceBuilder theDelegate, java.lang.String theSource)
           
 
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

PROPERTY_GENBANK_ACCESSIONS

public static final java.lang.String PROPERTY_GENBANK_ACCESSIONS
See Also:
Constant Field Values

features

protected FeatureTableParser features
Constructor Detail

GenbankProcessor

public GenbankProcessor(SequenceBuilder theDelegate,
                        java.lang.String theSource)

GenbankProcessor

public GenbankProcessor(SequenceBuilder theDelegate)
Method Detail

endSequence

public void endSequence()
                 throws ParseException
Description copied from interface: SeqIOListener
Notify the listener that processing of the sequence is complete.

Specified by:
endSequence in interface SeqIOListener
Overrides:
endSequence in class SequenceBuilderFilter
Throws:
ParseException

addSequenceProperty

public void addSequenceProperty(java.lang.Object key,
                                java.lang.Object value)
                         throws ParseException
Description copied from interface: SeqIOListener
Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.

Specified by:
addSequenceProperty in interface SeqIOListener
Overrides:
addSequenceProperty in class SequenceBuilderFilter
Throws:
ParseException

addParseErrorListener

public void addParseErrorListener(ParseErrorListener theListener)
Adds a parse error listener to the list of listeners if it isn't already included.

Specified by:
addParseErrorListener in interface ParseErrorSource
Parameters:
theListener - Listener to be added.

removeParseErrorListener

public void removeParseErrorListener(ParseErrorListener theListener)
Removes a parse error listener from the list of listeners if it is included.

Specified by:
removeParseErrorListener in interface ParseErrorSource
Parameters:
theListener - Listener to be removed.

notifyParseErrorEvent

protected void notifyParseErrorEvent(ParseErrorEvent theEvent)
Passes the event on to all the listeners registered for ParseErrorEvents.

Parameters:
theEvent - The event to be handed to the listeners.