org.biojava.bio.seq.io

Class SwissprotProcessor

java.lang.Object

org.biojava.bio.seq.io.SequenceBuilderFilter

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

Nested Classes

Modifier and Type	Class and Description
static class	SwissprotProcessor.Factory Deprecated. Factory which wraps SequenceBuilders in a SwissprotProcessor

Field Summary

Fields

Modifier and Type	Field and Description
static String	PROPERTY_SWISSPROT_ACCESSIONS Deprecated.
static String	PROPERTY_SWISSPROT_COMMENT Deprecated.
static String	PROPERTY_SWISSPROT_FEATUREATTRIBUTE Deprecated.

Constructor Summary

Constructors

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

Method Summary

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_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.