Package org.biojava.bio.seq.io
Interface SeqIOListener
- 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 the
RichSeqIOListener
.- Since:
- 1.1
- Author:
- Thomas Down, Matthew Pocock
- See Also:
-
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.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.
-
Method Details
-
startSequence
Start the processing of a sequence. This method exists primarily to enforce the life-cycles of SeqIOListener objects.- Throws:
ParseException
-
endSequence
Notify the listener that processing of the sequence is complete.- Throws:
ParseException
-
setName
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
-
setURI
Notify the listener of a URI identifying the current sequence.- Throws:
ParseException
-
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.
-
addSequenceProperty
Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.- Throws:
ParseException
-
startFeature
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
-
endFeature
Mark the end of data associated with one specific feature.- Throws:
ParseException
-
addFeatureProperty
Notify the listener of a feature property.- Throws:
ParseException
-