Package org.biojava.bio.seq.io
Class GenbankProcessor
java.lang.Object
org.biojava.bio.seq.io.SequenceBuilderFilter
org.biojava.bio.seq.io.GenbankProcessor
- All Implemented Interfaces:
SeqIOListener
,SequenceBuilder
,ParseErrorSource
- Direct Known Subclasses:
ProteinRefSeqProcessor
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Simple filter which handles attribute lines from a Genbank file
- Author:
- Greg Cox
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
Deprecated.Factory which wraps sequence builders in a GenbankProcessor -
Field Summary
FieldsModifier and TypeFieldDescriptionprotected FeatureTableParser
Deprecated.static final String
Deprecated. -
Constructor Summary
ConstructorsConstructorDescriptionGenbankProcessor
(SequenceBuilder theDelegate) Deprecated.GenbankProcessor
(SequenceBuilder theDelegate, String theSource) Deprecated. -
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
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Field Details
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PROPERTY_GENBANK_ACCESSIONS
Deprecated.- See Also:
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features
Deprecated.
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Constructor Details
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GenbankProcessor
Deprecated. -
GenbankProcessor
Deprecated.
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Method Details
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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
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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
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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.
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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.
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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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