org.biojava.bio.seq.io
Class SwissprotProcessor

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

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

public class SwissprotProcessor
extends SequenceBuilderFilter
implements ParseErrorSource

Simple filter which handles attribute lines from an Swissprot entry. Skeleton implementation, please add more functionality.

FIXME: Note that this is currently rather incomplete, and doesn't handle any of the header information sensibly except for ID and AC.

Since:
1.1
Author:
Thomas Down, Matthew Pocock, Greg Cox

Nested Class Summary
static class SwissprotProcessor.Factory
          Deprecated. Factory which wraps SequenceBuilders in a SwissprotProcessor
 
Field Summary
static String PROPERTY_SWISSPROT_ACCESSIONS
          Deprecated.  
static String PROPERTY_SWISSPROT_COMMENT
          Deprecated.  
static String PROPERTY_SWISSPROT_FEATUREATTRIBUTE
          Deprecated.  
 
Constructor Summary
SwissprotProcessor(SequenceBuilder delegate)
          Deprecated.  
SwissprotProcessor(SequenceBuilder delegate, String theSource)
          Deprecated. Constructor that sets the source of the feature to theSource.
 
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_SWISSPROT_ACCESSIONS

public static final String PROPERTY_SWISSPROT_ACCESSIONS
Deprecated. 
See Also:
Constant Field Values

PROPERTY_SWISSPROT_COMMENT

public static final String PROPERTY_SWISSPROT_COMMENT
Deprecated. 
See Also:
Constant Field Values

PROPERTY_SWISSPROT_FEATUREATTRIBUTE

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

SwissprotProcessor

public SwissprotProcessor(SequenceBuilder delegate,
                          String theSource)
Deprecated. 
Constructor that sets the source of the feature to theSource.

Parameters:
delegate - The sequecence builder to be used in constructing the sequence
theSource - The source of the features. e.g. "SWISS-PROT", "TrEMBL"

SwissprotProcessor

public SwissprotProcessor(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.