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
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic classDeprecated.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 TypeMethodDescriptionvoidaddParseErrorListener(ParseErrorListener theListener) Deprecated.Adds a parse error listener to the list of listeners if it isn't already included.voidaddSequenceProperty(Object key, Object value) Deprecated.Notify the listener of a sequence-wide property.voidDeprecated.Notify the listener that processing of the sequence is complete.protected voidnotifyParseErrorEvent(ParseErrorEvent theEvent) Deprecated.Passes the event on to all the listeners registered for ParseErrorEvents.voidremoveParseErrorListener(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
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Field Details
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PROPERTY_SWISSPROT_ACCESSIONS
Deprecated.- See Also:
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PROPERTY_SWISSPROT_COMMENT
Deprecated.- See Also:
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PROPERTY_SWISSPROT_FEATUREATTRIBUTE
Deprecated.- See Also:
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Constructor Details
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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"
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SwissprotProcessor
Deprecated.
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Method Details
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endSequence
Deprecated.Description copied from interface:SeqIOListenerNotify the listener that processing of the sequence is complete.- Specified by:
endSequencein interfaceSeqIOListener- Overrides:
endSequencein classSequenceBuilderFilter- Throws:
ParseException
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addSequenceProperty
Deprecated.Description copied from interface:SeqIOListenerNotify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.- Specified by:
addSequencePropertyin interfaceSeqIOListener- Overrides:
addSequencePropertyin classSequenceBuilderFilter- Throws:
ParseException
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addParseErrorListener
Deprecated.Adds a parse error listener to the list of listeners if it isn't already included.- Specified by:
addParseErrorListenerin interfaceParseErrorSource- Parameters:
theListener- Listener to be added.
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removeParseErrorListener
Deprecated.Removes a parse error listener from the list of listeners if it is included.- Specified by:
removeParseErrorListenerin interfaceParseErrorSource- Parameters:
theListener- Listener to be removed.
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notifyParseErrorEvent
Deprecated.Passes the event on to all the listeners registered for ParseErrorEvents.- Parameters:
theEvent- The event to be handed to the listeners.
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