Package 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
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 ClassesModifier and TypeClassDescriptionstatic class
Deprecated.Factory which wraps SequenceBuilders in a SwissprotProcessor -
Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionSwissprotProcessor
(SequenceBuilder delegate) Deprecated.SwissprotProcessor
(SequenceBuilder delegate, String theSource) Deprecated.Constructor that sets the source of the feature to theSource. -
Method Summary
Modifier and TypeMethodDescriptionvoid
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
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
-
Field Details
-
PROPERTY_SWISSPROT_ACCESSIONS
Deprecated.- See Also:
-
PROPERTY_SWISSPROT_COMMENT
Deprecated.- See Also:
-
PROPERTY_SWISSPROT_FEATUREATTRIBUTE
Deprecated.- See Also:
-
-
Constructor Details
-
SwissprotProcessor
Deprecated.Constructor that sets the source of the feature to theSource.- Parameters:
delegate
- The sequecence builder to be used in constructing the sequencetheSource
- The source of the features. e.g. "SWISS-PROT", "TrEMBL"
-
SwissprotProcessor
Deprecated.
-
-
Method Details
-
endSequence
Deprecated.Description copied from interface:SeqIOListener
Notify the listener that processing of the sequence is complete.- Specified by:
endSequence
in interfaceSeqIOListener
- Overrides:
endSequence
in classSequenceBuilderFilter
- Throws:
ParseException
-
addSequenceProperty
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 interfaceSeqIOListener
- Overrides:
addSequenceProperty
in classSequenceBuilderFilter
- Throws:
ParseException
-
addParseErrorListener
Deprecated.Adds a parse error listener to the list of listeners if it isn't already included.- Specified by:
addParseErrorListener
in interfaceParseErrorSource
- Parameters:
theListener
- Listener to be added.
-
removeParseErrorListener
Deprecated.Removes a parse error listener from the list of listeners if it is included.- Specified by:
removeParseErrorListener
in interfaceParseErrorSource
- Parameters:
theListener
- Listener to be removed.
-
notifyParseErrorEvent
Deprecated.Passes the event on to all the listeners registered for ParseErrorEvents.- Parameters:
theEvent
- The event to be handed to the listeners.
-