org.biojava.bio.seq.io
Class EmblProcessor

java.lang.Object
  extended by org.biojava.bio.seq.io.SequenceBuilderFilter
      extended by org.biojava.bio.seq.io.EmblProcessor
All Implemented Interfaces:
SeqIOListener, SequenceBuilder, ParseErrorSource

Deprecated. Use org.biojavax.bio.seq.io framework instead

public class EmblProcessor
extends SequenceBuilderFilter
implements ParseErrorSource

Simple filter which handles attribute lines from an EMBL file. This class delegates creation of Features 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).

Since:
1.1
Author:
Thomas Down, Greg Cox, Keith James

Nested Class Summary
static class EmblProcessor.Factory
          Deprecated. Factory which wraps SequenceBuilders in an EmblProcessor
 
Field Summary
static 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(Object key, 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

PROPERTY_EMBL_ACCESSIONS

public static final String PROPERTY_EMBL_ACCESSIONS
Deprecated. 
See Also:
Constant Field Values
Constructor Detail

EmblProcessor

public EmblProcessor(SequenceBuilder delegate)
Deprecated. 
Method Detail

endSequence

public void endSequence()
                 throws ParseException
Deprecated. 
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(Object key,
                                Object value)
                         throws ParseException
Deprecated. 
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)
Deprecated. 
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)
Deprecated. 
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)
Deprecated. 
Passes the event on to all the listeners registered for ParseErrorEvents.

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