Package org.biojava.bio.seq.io
Class EmblProcessor
java.lang.Object
org.biojava.bio.seq.io.SequenceBuilderFilter
org.biojava.bio.seq.io.EmblProcessor
- All Implemented Interfaces:
SeqIOListener
,SequenceBuilder
,ParseErrorSource
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Simple filter which handles attribute lines from an EMBL file. This
class delegates creation of
Feature
s to a
FeatureTableParser
, which in turn delegates creation
of Locations
to an EmblLikeLocationParser
which is shared with the GenbankProcessor
.
An EmblLikeLocationParser
parses EMBL/Genbank style
locations. Supported location forms:
123 invalid input: '<'123 or >123 (123.567) (123.567)..789 123..(567.789) (123.345)..(567.789) 123..456 invalid input: '<'123..567 or 123..>567 or invalid input: '<'123..>567 123^567 AL123465:(123..567)The only EMBL header information retained over a read/write cycle is the accession number (all numbers).
- Since:
- 1.1
- Author:
- Thomas Down, Greg Cox, Keith James
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
Deprecated.Factory which wraps SequenceBuilders in an EmblProcessor -
Field Summary
Fields -
Constructor Summary
Constructors -
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
-
PROPERTY_EMBL_ACCESSIONS
Deprecated.- See Also:
-
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Constructor Details
-
EmblProcessor
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
-
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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