Package org.biojava.bio.seq.io
Class SeqIOFilter
java.lang.Object
org.biojava.bio.seq.io.SeqIOFilter
- All Implemented Interfaces:
SeqIOListener
Base-class for listeners that pass filtered events onto another listener.
- Since:
- 1.1
- Author:
- Matthew Pocock
- See Also:
-
Constructor Summary
ConstructorsConstructorDescriptionSeqIOFilter
(SeqIOListener delegate) Create a new SeqIOFilter that will forward events on to another listener. -
Method Summary
Modifier and TypeMethodDescriptionvoid
addFeatureProperty
(Object key, Object value) Notify the listener of a feature property.void
addSequenceProperty
(Object key, Object value) Notify the listener of a sequence-wide property.void
addSymbols
(Alphabet alpha, Symbol[] syms, int start, int length) Notify the listener of symbol data.void
Mark the end of data associated with one specific feature.void
Notify the listener that processing of the sequence is complete.Retrieve the delegate that is wrapped.void
Notify the listener that the current sequence is generally known by a particular name.void
Notify the listener of a URI identifying the current sequence.void
startFeature
(Feature.Template templ) Notify the listener that a new feature object is starting.void
Start the processing of a sequence.
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Constructor Details
-
SeqIOFilter
Create a new SeqIOFilter that will forward events on to another listener.- Parameters:
delegate
- the SeqIOListener to wrap
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-
Method Details
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getDelegate
Retrieve the delegate that is wrapped.- Returns:
- the SeqIOListener delegate
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startSequence
Description copied from interface:SeqIOListener
Start the processing of a sequence. This method exists primarily to enforce the life-cycles of SeqIOListener objects.- Specified by:
startSequence
in interfaceSeqIOListener
- Throws:
ParseException
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endSequence
Description copied from interface:SeqIOListener
Notify the listener that processing of the sequence is complete.- Specified by:
endSequence
in interfaceSeqIOListener
- Throws:
ParseException
-
setName
Description copied from interface:SeqIOListener
Notify the listener that the current sequence is generally known by a particular name.- Specified by:
setName
in interfaceSeqIOListener
- Parameters:
name
- the String that should be returned by getName for the sequence being parsed- Throws:
ParseException
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setURI
Description copied from interface:SeqIOListener
Notify the listener of a URI identifying the current sequence.- Specified by:
setURI
in interfaceSeqIOListener
- Throws:
ParseException
-
addSymbols
public void addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) throws IllegalAlphabetException Description copied from interface:SeqIOListener
Notify the listener of symbol data. All symbols passed to this method are guarenteed to be contained within the specified alphabet. Generally all calls to a given Listener should have the same alphabet -- if not, the listener implementation is likely to throw an exception- Specified by:
addSymbols
in interfaceSeqIOListener
- Parameters:
alpha
- The alphabet of the symbol datasyms
- An array containing symbolsstart
- The start offset of valid data within the arraylength
- The number of valid symbols in the array- Throws:
IllegalAlphabetException
- if we can't cope with this alphabet.
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addSequenceProperty
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
- Throws:
ParseException
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startFeature
Description copied from interface:SeqIOListener
Notify the listener that a new feature object is starting. Every call to startFeature should have a corresponding call to endFeature. If the listener is concerned with a hierarchy of features, it should maintain a stack of `open' features.- Specified by:
startFeature
in interfaceSeqIOListener
- Throws:
ParseException
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endFeature
Description copied from interface:SeqIOListener
Mark the end of data associated with one specific feature.- Specified by:
endFeature
in interfaceSeqIOListener
- Throws:
ParseException
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addFeatureProperty
Description copied from interface:SeqIOListener
Notify the listener of a feature property.- Specified by:
addFeatureProperty
in interfaceSeqIOListener
- Throws:
ParseException
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