Package org.biojava.bio.seq.io
Interface SeqIOListener
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- All Known Subinterfaces:
RichSeqIOListener
,RichSequenceBuilder
,SeqFileFormer
,SequenceBuilder
- All Known Implementing Classes:
DebuggingRichSeqIOListener
,EmblFileFormer
,EmblProcessor
,FastaDescriptionLineParser
,GenbankFileFormer
,GenbankProcessor
,OrganismParser
,ProteinRefSeqFileFormer
,ProteinRefSeqProcessor
,RichSeqIOAdapter
,SeqIOAdapter
,SeqIOFilter
,SequenceBuilderBase
,SequenceBuilderFilter
,SequenceDBSequenceBuilder
,SimpleAssemblyBuilder
,SimpleRichSequenceBuilder
,SimpleSequenceBuilder
,SmartSequenceBuilder
,SwissprotFileFormer
,SwissprotProcessor
public interface SeqIOListener
Notification interface for objects which listen to a sequence stream parser. More functionality is offered by theRichSeqIOListener
.- Since:
- 1.1
- Author:
- Thomas Down, Matthew Pocock
- See Also:
RichSeqIOListener
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
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
endFeature()
Mark the end of data associated with one specific feature.void
endSequence()
Notify the listener that processing of the sequence is complete.void
setName(String name)
Notify the listener that the current sequence is generally known by a particular name.void
setURI(String uri)
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
startSequence()
Start the processing of a sequence.
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Method Detail
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startSequence
void startSequence() throws ParseException
Start the processing of a sequence. This method exists primarily to enforce the life-cycles of SeqIOListener objects.- Throws:
ParseException
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endSequence
void endSequence() throws ParseException
Notify the listener that processing of the sequence is complete.- Throws:
ParseException
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setName
void setName(String name) throws ParseException
Notify the listener that the current sequence is generally known by a particular name.- Parameters:
name
- the String that should be returned by getName for the sequence being parsed- Throws:
ParseException
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setURI
void setURI(String uri) throws ParseException
Notify the listener of a URI identifying the current sequence.- Throws:
ParseException
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addSymbols
void addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) throws IllegalAlphabetException
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- 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
void addSequenceProperty(Object key, Object value) throws ParseException
Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.- Throws:
ParseException
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startFeature
void startFeature(Feature.Template templ) throws ParseException
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.- Throws:
ParseException
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endFeature
void endFeature() throws ParseException
Mark the end of data associated with one specific feature.- Throws:
ParseException
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addFeatureProperty
void addFeatureProperty(Object key, Object value) throws ParseException
Notify the listener of a feature property.- Throws:
ParseException
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