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java.lang.Objectorg.biojava.bio.seq.io.SequenceBuilderFilter
org.biojava.bio.seq.io.SwissprotProcessor
public class SwissprotProcessor
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.
Nested Class Summary | |
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static class |
SwissprotProcessor.Factory
Deprecated. Factory which wraps SequenceBuilders in a SwissprotProcessor |
Field Summary | |
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static String |
PROPERTY_SWISSPROT_ACCESSIONS
Deprecated. |
static String |
PROPERTY_SWISSPROT_COMMENT
Deprecated. |
static String |
PROPERTY_SWISSPROT_FEATUREATTRIBUTE
Deprecated. |
Constructor Summary | |
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SwissprotProcessor(SequenceBuilder delegate)
Deprecated. |
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SwissprotProcessor(SequenceBuilder delegate,
String theSource)
Deprecated. Constructor that sets the source of the feature to theSource. |
Method Summary | |
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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 |
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addFeatureProperty, addSymbols, endFeature, getDelegate, makeSequence, setName, setURI, startFeature, startSequence |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String PROPERTY_SWISSPROT_ACCESSIONS
public static final String PROPERTY_SWISSPROT_COMMENT
public static final String PROPERTY_SWISSPROT_FEATUREATTRIBUTE
Constructor Detail |
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public SwissprotProcessor(SequenceBuilder delegate, String theSource)
delegate
- The sequecence builder to be used in constructing the
sequencetheSource
- The source of the features. e.g. "SWISS-PROT", "TrEMBL"public SwissprotProcessor(SequenceBuilder delegate)
Method Detail |
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public void endSequence() throws ParseException
SeqIOListener
endSequence
in interface SeqIOListener
endSequence
in class SequenceBuilderFilter
ParseException
public void addSequenceProperty(Object key, Object value) throws ParseException
SeqIOListener
addSequenceProperty
in interface SeqIOListener
addSequenceProperty
in class SequenceBuilderFilter
ParseException
public void addParseErrorListener(ParseErrorListener theListener)
addParseErrorListener
in interface ParseErrorSource
theListener
- Listener to be added.public void removeParseErrorListener(ParseErrorListener theListener)
removeParseErrorListener
in interface ParseErrorSource
theListener
- Listener to be removed.protected void notifyParseErrorEvent(ParseErrorEvent theEvent)
theEvent
- The event to be handed to the listeners.
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