org.biojava.bio.seq.io

Class EmblProcessor

java.lang.Object

org.biojava.bio.seq.io.SequenceBuilderFilter

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

Nested Classes

Modifier and Type	Class and Description
static class	EmblProcessor.Factory Deprecated. Factory which wraps SequenceBuilders in an EmblProcessor

Field Summary

Fields

Modifier and Type	Field and Description
static String	PROPERTY_EMBL_ACCESSIONS Deprecated.

Constructor Summary

Constructors

Constructor and Description
EmblProcessor(SequenceBuilder delegate) Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
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.